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If you have the right cable, try running the analogue output of the Express to an input on the pre amp. This will tell you if it's a network issue or a cable issue.
You're not alone with this problem...
There's a lot of info available on Computer Audiophile and other websites to help troubleshooting this. Google "Apple Airport Express Streaming Issues"
I'm running AE (7.6.8) with no issues. I had Wi-Fi drops until I switched to 5GHz router (dual band). The only thing I can think of is, that either optical mini plug on the Toslink cable, or mini/Toslink adaptor (I use adaptor) have bad contact (too much distance) or dirt - causing reduction in light intensity. Try different Toslink cable or different adaptor.
sprayed the airport express and the toslink input on the DAC with canned air. Still getting skipping using my minijack to toslink cable. I ordered a minijack to RCA spdif cable before seeing your post.
if that doesn't work, the problem may be the airport express jack - i should try another airport express, huh.
i do like the look of the toslink/miniplug glass fiber cable at lifatec