I have a Rogers d803 in canada. No matter what ROM I am on (tried Stock, Cloudy 3.3, 2.2, Cloudy stock 2.7) I have this annoying as heck problem where I will not receive texts for a few hours and then they will all come in at the same time in bunches. Every 2-3 hours my phone will vibrate apocalyptically since it gets flooded with all the texts i didnt get at once.
Are you sure it's related to your ROMs? What carrier are you on? I had this issue not infrequently when I was with Mobilicity, and it resolved as soon as I switched to Rogers.