How many minutes should the ACEMD - GPU molecular dynamics 6.03 (cuda) WU last? I am using Nvidia GTX 275 card and the latest drivers. Currently: 20 minutes and only 4%. Is this ok?

That is about the time you might expect.

Does the checkpointing work?

Yes it does.

Yes that's fine. The time elapsed for prcentage done is not linear. Checkpointing does work.
When and if the unit completes you will be able to get the time per step for the unit and compare it to another machine that has done a similar unit on the same card. Post it here and someone will tell you.

HTH you could try updating your cards drivers.

Why are these WUs failing?

You have to link them to your host, as links for users results are only valid for the user him/herself. As you only have one host, and that one not hidden, it wasn't that hard to guess ;)

Just to show yo, here are mine: user and host.

PCIe 1 16x delivers plenty of speed for GPU-Grid. If you're loosing anything it's well below measurement error / accuracy (normal spread in WU times).

The GTX275 of a friend used to get ~20k RAC here, but due to the recent improvements to the client this value is going up. It has reached 24k by now and if I project speed based on 1 sample WU it would reach 34k RAC (seems a bit too high). Assuming the machine is crunching 24/7.

BTW: running a Pentium D is quite inefficient, as it's very slow for the power it consumes. Sadly your board doesn't support Core 2 CPUs. If I were you I'd stop crunching on the Pentium D to save energy cost. The GPU will more than make up for it ;)

MrS