Which pool?  For Urays pool, the number of shares submitted for a plot is irrelevant.  It progressively scans for better shares across all the plots only submitting one if it finds one better than the previous one.  Ideally the miner would only submit one share for the entire miner per block, but as a new block could be detected before we have finished scanning all the plots we want to submit the best shares as we find them so we get credit.

For the official pool, yes you would expect to find more shares for a large plot than a small one, but a large plot has more of a chance to get interrupted than a small one, especially if the large plot is towards the end of the list of scanned plots.  For instance on one of my miners 1 have 11 90gb plots... The last 2 plots get interrupted all the time, which means they are not completely scanned all the time, and so would produce less shares than the ones that are always scanned.

I don think there is a bug here, but I'll keep an eye out on my miners and see if I see any pattern.

Do you have a screen shot of the "system" view showing the plots and stats? I would be interested to see it.  You could pm the image if you don't want to have it out in public.