Are you sure that your sequence frame rate matches
the frame rate of your footage?
The original frame rate of my footage is 1080 25fps (50i) (PAL).
I imported the clip into After Effects and converted it in 1080p (25fps progressive) and then I imported it into Premiere PRO CS5.
The premiere sequence is 1080 25p. So, yes, both clip and sequence have the same frame rates.
I think if I import the original 1080 25fps (50i) (PAL) clip in a 1080 25fpm (50i) sequence, I don't have the problem, but sometimes I do...
Anyway, there is a certain solution to this problem. Either you know it or you don't. I just don't remember it and I cannot find the relevant tutorial...
I don't recall anyone ever posting about this specific issue here in these forums. Certainly it's not normal or common behavior.
Out of curiosity, why the conversion from 25i to 25p? As only the former can be put onto Blu-ray, it may be better to work with the original unaltered media. Or for web delivery, it still may be better to work with the 25i, letting the export options do the "progressive" conversion for you.