RAM is more complicated then they seem to be now. There is the format of ddr, ddr2, and ddr3. There is different speed, and different latency on the ram too.
The possible reason of the slow down might be:
The 512 ram is slower than the rest of ram
The size of 512mb is inefficient comparing to the larger size installed in other slots
DDR2 ram are recommended to run in pairs to provide better performance
just my .02
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