Wookiee
You probably will not like to hear this but there is quite a bit of evidence that Xeon CPU's are not best suited to music production.  Great server processors but........

Do you have some info on this??
tia
rafone

Zargg71
Do you have the latest ASIO drivers for your AI?
Did you try latencymon, to see if there are anything that sticks out?

Yes on the drivers......
Don't have the problem until after a plugin

JonD
Definitely not the norm.  You're sure these are normal FX with no lookahead feature (that tend to add latency)?  I'm speaking of FX like convolution reverbs, linear phase dynamics like CW's LP-- fx, etc...

Here is an example
Track1    Lead Guitar
Track2    Rhythm Guitar
Track3    Bass Guitar
Track4
Track5   AD2 single synth Drums
 
All these tracks are put down the old fashion way with a
1. simple drum click track     .... route to a drum bus
2. then the dry rhythm track ... route to a guitar bus
3. then the bass                   ... route to bass bus
4 then the lead....                ... route to guitar bus
 
then mix for adequate gains using the gain knob...to get rough mix
 
save etc
 
Now as long as this is the project that I use I can add or fix pieces and everything will sync as you would expect.
Then if I add the simplest thing to a track lets say concrete limiter or PC4K S Type Bus Comp then anything I add or fix is not in sync.......
 
thx
rafone