Lots of run problems that develop with the CB550 are solved with a complete and thorough tuneup. This should be done every 3000 miles anyway, but certainly before any carburetor adjustments are made.
If the tuneup doesn't cure the problem then it's probably time to sync the carbs.
Have you checked for fuel contamination? Or, air leaks between carb and head.
Also, unless you mention changes, we always assume a stock configured bike. Modified bikes frequently need different adjustments.
Cheers,