some of the blocks of my 'sieve' type mob farm have sort of disappeared but cannot be replaced

I have a 'sieve' type mob farm that has facing rows of pistons that alternate pushing floors one way and then aonther to allow mobs to fall through. I noticed it wasn't operating properly - and went up inside -to find many of the floor and piton blocks had become completely transparent, and mobs fell through the spaces as though they weren't there BUT I could not replace the missing blocks as the spaces acted as though they were still occupied - and faint outlines are still in place -like when a tripwire is present... Trying to remove the transparent blocks with a pickaxe produced appropriate coloured particales, but the missing block would not break. I was running rei's minimap and a recent installation of optifine to try and improve framerates -had really bad problems with frame rate crashes in some locations -so I re-installed an older save and removed mods. Problems persists though, -with fewer of the 'missing blocks' but still a problem... Frame rates creashing also a problem. Is this a bug, or chunk/ world corruption, or a combination of things?