This sounds to me like you may be conflating Aura and Aria?
It looks like I was conflating the names.
I am not clear on any of this unfortunately, are you saying that RGMercs starting memorizing more songs than it had previously, and you didn't change any options that would lead it to do so? I am unclear as to why you would be manually removing songs.
The first thing that brought my attention to the problem was that the toon was constantly memming spells. As I noticed the note whenever I load that the spell gems equal the loadout, I first started removing options for the loadout to bring it below the gem count. This worked to stop the constantly memming spells. But I think this was just a symptom of the issue and not the issue.
My theory on this is likely that you paused automation while your dps aura was memorized and this caused the dps aura to become the new "default" gem for that slot as far as the automation was concerned. So when the regen aura was cast and wouldn't stick (because you still had an aura active), the automation placed the old gem back in the slot, as it is programmed to do. In this case, unfortunately, doing a spell loadout check every time you unpaused would be disastrous to automation, so it is best not to manually adjust spells while paused (unless you are purposefully taking advantage of this "feature", which I actually do upon occasion).
When it first started to happen I did pause to make it stop and try and figure out what was happening. Later in my tests, from logging in from the character select I did not pause. The log I attached it from loading from character select, so it shows all the modules unloading and loading.
While this may seem like a good idea, swapping the aura options already triggers a loadout change, which amounts to the same thing and when done rapidly it can really bog things down and cause some conflicting actions to occur.
I found it was having a problem with the DPS aura, so I changed it to the Regen aura, and still had the same problem. When changing to NONE, it might have caused what you are suggesting and bogged down the system.
Overall, I guess I would like to ask if you are still having issues, and if so, I can attempt to assist in resolving them. Please note that RGL isn't set up to remove auras, but perhaps we can consider if it was feasible to implement.
I can test more later tonight when I get home.
But one thing not mentioned is the ranking of the aura, which you can't see on a 120 toon for a level 125 and 122 auras (I don't know if the lower spells have the same issue). The gold account toon was casting rank 2 auras, with rank 1 effects landing.
[BARD_TOON

EBUG (rgmercs_utils.
Lua::SetLoadOut():3527)] <237126.350> Finding best spell for Set: BardDPSAura
[BARD_TOON

EBUG (rgmercs_utils.
Lua::GetBestSpell():571 )] <237126.469> Found Aura of Tenisbre level(125) rank(Aura of Tenisbre Rk. II)
[BARD_TOON

EBUG (rgmercs_utils.
Lua::SetLoadOut():3527)] <237126.469> Finding best spell for Set: BardRegenAura
[BARD_TOON

EBUG (rgmercs_utils.
Lua::GetBestSpell():571 )] <237126.585> Found Aura of Shalowain level(122) rank(Aura of Shalowain Rk. II)
[BARD_TOON:VERBOSE(class.
Lua::unknown_func():700 )] <237131.196> :::RUN ROTATION::: 3281 => Downtime
[BARD_TOON:VERBOSE(rgmercs_utils.
Lua::RunRotation():1381)] <237131.212> Doing RunRotation(start(0), step(0), cur(1))
[BARD_TOON:VERBOSE(rgmercs_utils.
Lua::TestConditionForEntry():1340)] <237131.228> :: Testing Condition for entry(BardDPSAura) type(Song) cond(s, Aura of Tenisbre, BARD_TOON) ==> true
[BARD_TOON

EBUG (rgmercs_utils.
Lua::UseSong():940 )] <237131.228> UseSong(Aura of Tenisbre Rk. II, 3281, true)
[BARD_TOON:VERBOSE(rgmercs_utils.
Lua::UseSong():999 )] <237131.243> Aura of Tenisbre Rk. II =>> BARD_TOON <<=
[BARD_TOON

EBUG (rgmercs_utils.
Lua:

oCmd():1972)] <237131.243> RGMercs sent MQ Command: >> /cast "Aura of Tenisbre Rk. II" <<
[BARD_TOON

EBUG (rgmercs_utils.
Lua:

oCmd():1972)] <237132.171> RGMercs sent MQ Command: >> /stopsong <<
[BARD_TOON

EBUG (rgmercs_utils.
Lua::ExecEntry():1243)] <237132.172> Trying To Cast BardDPSAura - Aura of Tenisbre Rk. II :: Failed!
<---- note, aura of tenisbre effect 1 was in the aura window
[BARD_TOON:VERBOSE(rgmercs_utils.
Lua::RunRotation():1381)] <237132.187> Doing RunRotation(start(0), step(0), cur(2))
[BARD_TOON:VERBOSE(rgmercs_utils.
Lua::TestConditionForEntry():1340)] <237132.188> :: Testing Condition for entry(BardRegenAura) type(Song) cond(s, Aura of Shalowain, BARD_TOON) ==> false
[BARD_TOON:VERBOSE(rgmercs_utils.
Lua::RunRotation():1400)] <237132.203> Failed Condition RunRotation(start(0), step(0), cur(2))
[BARD_TOON:VERBOSE(rgmercs_utils.
Lua::RunRotation():1381)] <237132.203> Doing RunRotation(start(0), step(0), cur(3))
a couple seconds later
[BARD_TOON:VERBOSE(rgmercs_utils.
Lua::RunRotation():1381)] <237144.193> Doing RunRotation(start(0), step(0), cur(1))
[BARD_TOON:VERBOSE(rgmercs_utils.
Lua::TestConditionForEntry():1340)] <237144.218> :: Testing Condition for entry(BardDPSAura) type(Song) cond(s, Aura of Tenisbre, BARD_TOON) ==> true
[BARD_TOON

EBUG (rgmercs_utils.
Lua::UseSong():940 )] <237144.218> UseSong(Aura of Tenisbre Rk. II, 3281, true)
[BARD_TOON:VERBOSE(rgmercs_utils.
Lua::UseSong():999 )] <237144.243> Aura of Tenisbre Rk. II =>> BARD_TOON <<=
[BARD_TOON

EBUG (rgmercs_utils.
Lua:

oCmd():1972)] <237144.243> RGMercs sent MQ Command: >> /cast "Aura of Tenisbre Rk. II" <<
[BARD_TOON

EBUG (rgmercs_utils.
Lua::SetLastCastResult():1660)] <237144.686> Set Last Cast Result => CAST_DISTRACTED
[BARD_TOON

EBUG (rgmercs_utils.
Lua:

oCmd():1972)] <237145.233> RGMercs sent MQ Command: >> /stopsong <<
[BARD_TOON

EBUG (rgmercs_utils.
Lua::ExecEntry():1243)] <237145.233> Trying To Cast BardDPSAura - Aura of Tenisbre Rk. II :: Failed!
[BARD_TOON:VERBOSE(rgmercs_utils.
Lua::RunRotation():1381)] <237145.257> Doing RunRotation(start(0), step(0), cur(2))
a couple seconds later
[BARD_TOON:VERBOSE(rgmercs_utils.
Lua::RunRotation():1381)] <237146.159> Doing RunRotation(start(0), step(0), cur(1))
[BARD_TOON:VERBOSE(rgmercs_utils.
Lua::TestConditionForEntry():1340)] <237146.183> :: Testing Condition for entry(BardDPSAura) type(Song) cond(s, Aura of Tenisbre, BARD_TOON) ==> true
[BARD_TOON

EBUG (rgmercs_utils.
Lua::UseSong():940 )] <237146.184> UseSong(Aura of Tenisbre Rk. II, 3281, true)
[BARD_TOON:VERBOSE(rgmercs_utils.
Lua::UseSong():999 )] <237146.207> Aura of Tenisbre Rk. II =>> BARD_TOON <<=
[BARD_TOON

EBUG (rgmercs_utils.
Lua:

oCmd():1972)] <237146.207> RGMercs sent MQ Command: >> /cast "Aura of Tenisbre Rk. II" <<
[BARD_TOON

EBUG (rgmercs_utils.
Lua::SetLastCastResult():1660)] <237146.667> Set Last Cast Result => CAST_DISTRACTED
[BARD_TOON

EBUG (rgmercs_utils.
Lua:

oCmd():1972)] <237147.198> RGMercs sent MQ Command: >> /stopsong <<
[BARD_TOON

EBUG (rgmercs_utils.
Lua::ExecEntry():1243)] <237147.199> Trying To Cast BardDPSAura - Aura of Tenisbre Rk. II :: Failed!
repeat ad nauseam
Meanwhile
You do not have sufficient focus to maintain that ability. was filling up my chat window. <-- This did not happen before the patch.
More to come.