Cross dissolve error in Permiere Pro
You didn't mention which version of PPro you are using; but in version CS6 and prior there IS a bug with cross dissolve which is a bit idiosyncratic. 

The fix; move all of your video (select all) up one layer. 

Then add black video; or a color matte (black) which is the length of your program to the bottom (first) video track. 

This in essence resets all the preview files PPro has generated; (which I believe is where the problem is). 

If this doesn't work; you could try changing the default transition from cross dissolve to film dissolve... the visual effect is not "identical" but I don't think it would be a deal breaker if my first suggestion doesn't work for you. 

Last option; you can pull the clips in; and out; using Trim; and make sure you make sure the dissolve rests on a new different frame on the timeline. + or - 1 frame to the left or right. 

But yes; I have seen this; and it's why all our editors now cut starting on layer 2; and the last step of the process; is we lay black under the entire program before output.