Sorry to rate so low...
I just don't want to give a high review for a test of noises.
I am still new to FL myself, I would say the best way to keep your beats lined up correctly is to use the beat sequencer, you can extend it by upping the number at the top left LED panel that has "- -" in it. One thing I have a problem with is when putting my beats in the playlist if I do not click the mouse exactly the same way each time I notice I have small gaps in between my inserts, maybe that's your issue? I don't know how to get around this other than having a lot of patience, lol. The paint tool sometimes doesn't insert how I need it either...
Just keep messing around with playlist and step sequencer, there are some videos on youtube and wonderhowto.com that really helped me through that area.