I have the same error on X-surf100 with Rapidroad attached - "nak timeout". So far I tried it on A4000D+Warpengine and A4000T + CS 060 MkII. Using clean WB 3.1 (with only MUI 3.8 installed) and also on 3.9 (ClassicWB). I had RTG drivers on both though (Picasso96 on one and CGX 3 on other). Tried the Z2 pins on X-surf - same result. Both machines have Buster 11 and X-surf alone works ok.
No problems over clockport on A1200.