The answers above are correct. If you have the taller milspec F-marked FSB on a flat top then you should buy a milspec height rear sight or carry handle.
If your flat top has the shorter A2 height FSB you still should go with a milspec height rear sight or carry handle (for compatibility) and buy the Bushmaster 0.04" taller front sight post to bring the front sight up to milspec height.
I did this to my ArmaLite middy and it solved the problem nicely and permanently. The other option is buy a shorter commercial height rear sight or carry handle as mic_poo pointed out but you'd always have to worry about this when changing out the rear irons. Instead I'd go with the taller sight post as it's only $5.50 or so. One problem with this is on some FSBs the taller post sticks slightly above the protective ears. Don't know which brands are like that but it wasn't an issue with my ArmaLite.
Annoying problem you have to be aware of with ArmaLite, DPMS, Bushmaster and a few others. Technically Colt is to blame for this, they should have kept the A2 height FSB for flat tops and just shortened the rear sights to fit. Then it wouldn't matter which upper receiver a barrel/FSB is put on.