Update: Today I completely rebuilt my miggy from scratch on my SanDisk 4GB 30mb/s CF card (instead of the Kingston 4GB) but even with a 200mb System Partition and 2 other partitions (1.9GB & 1.7GB), again using PFS3, the speed issue remains (it's not faster or slower).
Im waiting on a new rev8a Mobo, 1mb trapdoor card and 8mb auto-config ram board so it'l be interesting to see if anything changes then.