Rotarycraft apparently messing up my world, what can i do about it?

I recently added Rotary Craft to my 1.4.7 world, and since then i have some weird issues. Yesterday it started getting bad, maybe you guys know how to fix these issues (other than by the obvious way of removing the mod again). These are the symptoms i am getting:

• Ender Storage: apparently, it stopped looking for the ender chest data in the right directory ( which for some reason is in the mystcraft limbo dimension's directory), and instead chose the ender storage directory under the root. I deleted those files, and got my items back. Later it seems the game just overwrote the data instead of ignoring it. So even worse...
• Graphics: From time to time, some rotarycraft blocks turn transparent (not invisible) and stay that way for minutes. This does not keep the blocks from working normal.
• block breaking / placing: sometimes, placing blocks doesn't work anymore. I need to restart the game then, and then find my items again in my inventory as if nothing happened. When i craft, upon closing and reopening the inventory, i find the original items. A few blocks seem to have vanished when i broke them, they didn't reappear on aggame restart.

What is causing this and is it possible to fix these issues?

My setup:

Minecraft 1.4.7 Every mod from Tekkit Lite Soul shards Optifine Rotary Craft