For anyone else who comes across this thread, I was able to solve my problem permanently by flashing a new PIT file. I found the correct PIT files for the GT-i9100 in this XDA thread
. It seemed my partitions had become messed up long ago, as the phone had been showing a 2GB /data partition and only a 2GB internal SD card partition (which should've been closer to 12GB) for some time.
I choose a 4GB data partition (since I was running low on /data space last time). Oddly enough, booting the stock ROM after flashing the PIT only showed a 2GB data partition. Once I flashed CM10 it showed as 4GB though.