I intended to play this game on a Wii with retroarch, it plays fullspeed except for this bit and it drops to 30-40fps
I managed to remove the effect thanks to you, however it still slows down. So that wasn't it.
I was led to believe this was the cause because the other FEs work fine and those don't use that effect, and when Nintendo released it on the 3DS without that effect I was certain... But you say it does have that effect.
This guy has footage of the change on a 3DS
http://youtu.be/UnDApoy6s4s?t=1m33s - skip to 1:33
I found another one that does have the flowys.
http://youtu.be/oBqC6Oi0CTw?t=1m9s - skip to 1:09
Also, it seems they all use the US version because of the lack of extra languages.
There is also the possibility that it's not full emulation for GBA games, the battery usage is the cause.
NES/GBC games reportedly use more battery consumption than GBA; this can only mean GBA runs natively or partly natively.
Looks like the edit is pretty random and without purpose.