It might be related to your computer specs. I had a lot of trouble initially with my older system - in spring 2000 as far as I remember. After upgrading my system the problems were gone.
I don't know if such is an option for you. I had good reasons to upgrade my system - and these were not games-related at all. It just turned out to be a welcome side-effect that suddenly those game problems were solved as well.
I remember that I wasn't able to play Infernal Machine for more than half an hour. Then the game started to do weird things. I had weverything ranging from gameplay and inventory problems to horrible crashes.
Later I read in some computer magazine about several incompatibilities of certain old AGP graphic cards - I had an old ATI these days, don't remember the exact type. The CPU was an AMD K6-2 (400 MHz or so) and the mainboard had an Aladdin V5 chipset. It was in fact that combination which caused the problems.
The "new" system is meanwhile pretty legacy. An ASUS Mainboard with an old Intel 440BX chipset and an Intel PIII 600E. The graphics card is a slow Matrox G400 with 32MB. It doesn't perform very well - but Infernal Machine runs without any glitches, with or without the patch. There are a few funny bugs, eg. when you use the chalk it sometimes happens that Indy starts swimming in the air. Harmless, anyway.
So if you like you could try to gather detailled info about your system (Windows version, CPU, mainboard, chipset, graphics card, RAM etc.). Maybe it's just a cheap component which can be replaced easily to solve your problems. Feel free to come back here, I'll try to advise you if you want and if time allows me to...