The way the the memory works on the Map Pro has the memory modules in slots 3 and 4 on each memory riser daisy-chained off of slots 1 and 2. This increases the time required to access memory on slots 3 and 4 and degrades performance. So by retaining those 512s (in slots 3 and 4 of the first memeory riser - as you want to put the 1 GB modules into slots 1 and 2 on each memory riser) you are going to see some drop off in memory performance.
In real life situations the real performance drop is negligible unless you have a memory-intesnive application running. Even then it will not be a disaster. The question is whether you are better off with another GB of memory (to stave off paging which does have a big impact on performance), or best to go for max memory performance by not using the 512s.
Some reading
http://www.hardwaresecrets.com/article/266
I also beleive I saw a note that 512 modules are single rank devices, where as 1GB modules (and bigger) use two ranks. Have to dig up a reference. If that is the case, then the bandwidth off those 512s is going to be half normal - another possible hit on performance. I do know when one rank went bad on a 1GB module the hardware cut out the matching rank on the other 1GB module and I found myself with only 3GB of memory until the bad 1GB module was replaced. One advantage of the FB-DIMMs and the server/workstation grade hardware was that my Mac Pro suffered not at all from the faulty memory.
The 512s were a cheep option by Apple (big surprise). Minimum memory in a Mac Pro should be 4 x 1GB.
😀
Ahhh.. Found it...
http://www.anandtech.com/mac/showdoc.aspx?i=2832