Before I get to an answer, and apologies for echoing what others are implying above, because you're
Running a relatively old version of Magento
Running a pre-release version of Magento
you're sort of off in the dessert by yourself. Beyond the obvious problems with your setup, most experienced Magento developers know that systems running an old version of the software are going to have countless system hacks and core customizations.
My guess if you're not actually clearing all your caches out — the only way to know for sure is to debug the configuration module loading and cache buildup in your system.
This old StackOverflow question has instructions for debugging setup resource problems. Start there. Per my guess, you may find that this part of the system can't see your setup resource configuration. If that's the case jump up to where the configuration is loaded and determine why it's not loading your configuration from cache.
I also threw together a module with a setup resource model that runs successfully on a stock 1.4.0.0-rc1 system. Try this one in your system and if you get the "Setup Resource is Loading" exception (which my setup resource script throws), then you know there's a problem that's specific to your module. Along those lines, its possible the scripting going on in your setup resource script acts different under cache and non-cache, and is being skipped by the system.
Good luck!