Does this happen in SSP too? I guess so, then please dont say its ONLY on Server.
"Only" 64 Cells? As far as I know the maximum StackSize in Minecraft is 64 (or 127 to be precicely).
I didn't know about SSP at the time because I didn't test it personally, I just had the report from one of my players on the server. Sorry about that, I give only the information I can directly confirm, I don't want to provide a misleading report. Plus it's a habit from too many years working in SQA writing so many bug reports, I only put the minimum information to recreate an issue.
But I did test it again just now and it is the same in both SSP and SMP. Empty cells only go to the leftmost slot on the bottom and once it fills with 64, any extras are gone.