There's not much space available in /system to begin with... on mine, with a fresh ROM install, it looks like there is only 98.17 MB available. The system folder is over 500 MB. That's intended to be a read only file system, so it doesn't need ANY available space. Any extra space in /system is unusable on a non-rooted device.
Dowloaded apps go in data (Over 800 MB available - displayed as Internal Storage in Android Settings) or internal SD Card (Over 5 GB available - displayed as NAND Storage in Android Settings).
Cache has over 200 MB available, for app settings and such...
Did all of your partitions mount correctly after flashing?
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