Hummm something sounds a little suspect a remap should make it run better and they are dead easy to do if you know what your doing. Assuming the OEM muffler has been replaced and both acro maps installed (there are 2 apparently) and the 15min reset has been done there should be no problem. Has anything else been done on the bike i.e. air filter changed, engine de-smogged?
If the engine was working fine prior to the remap with the stock muffler replaced and not afterwards then my money is on an incorrectly installed or incorrect map - it happens. Anyone with the right software and correct maps and who knows what they're doing can remap a 690...lots have. Good luck getting it sorted.
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