If you're lining the tracks up manually, I'm guessing that the WAVs are not being 'stretched', but are just being put in the wrong place once they're recorded?
If so then there's a way to fix it - I had a similar problem with a cheap'n'cheerful Tapco 2x2 i/f.
I'm using Cubase SX3, so possibly there'll be some differences with your setup, but here goes....
Open a new project, and set your time domain to Bars and Bears (right click on the ruler bar). Add an audio track and route a microphone to it, turn on the metronome (press C, or the CLICK button on the transport panel), point the mic at one of your monitors, arm the track and press record (MAKE SURE YOU'RE NOT MONITORING THE MIC SIGNAL!!!!!).
Let it run for a few bars, and you'll see spikes appear in your audio track corresponding to the click. Press stop. Zoom in a bit, and check whether these spikes line up exactly with the bar and beat lines on the ruler. If they do, then I've no idea what's causing your problem, sorry.
If they don't, then what's happening is your audio driver is over- or under-correcting for your system's latency and placing recorded audio in the wrong place.
Firstly, make sure you're using the correct driver (In the Devices menu, click Device Setup and open the VST Audio Bay section - check the Master ASIO Driver is the right one for your soundcard).
If that's all fine, you need to manually correct for the offset. Fortunately you can set this once and never have to think about it again, provided you always use the same sample rate.
Go back to your audio track, and zoom in so you can see a barline and the spike which corresponds to that barline (these are usually the high-pitched clicks). Turn on Snap-to-Bar and set your left locator to the barline. Turn off the snap and set your right locator to the very beginning of the spike, being as accurate as possible (this is assuming the spikes appear AFTER the corresponding barline, if the spikes are before the bar, use the L and R locators the other way round).
Once you've got your locators set, create a marker track and add a cycle marker (the button that looks like two P's - one backwards). You should end up with a cycle marker going from the barline to the spike (or vice-versa). Change your time domain back to seconds, select the cycle marker and you'll see in the info line how long the cycle is, and so the error Cubase is making (e.g. 27ms).
Almost there!
Now you need to figure out how many samples that is, which is simply:
(time in seconds) x (sample rate in Hz)
e.g. 0.027 x 44100 = 1190.7 samples
Go back to your VST Audio Bay and click the Expert button. Enter the nearest whole number of samples (1191 in this case) into the Record Placement Offset box. If your spikes are showing up BEFORE the barlines then this number needs to be negative.
Try recording the metronome again, and you should find the spikes match up with the barlines exactly.
The offset is obviously dependent on your sample rate, so it's a good idea to write the offset in milliseconds down somewhere so you don't need to go through the whole thing again if you do a project at e.g. 48kHz instead of 44.1kHz.
Hope that helps. Sorry it's such a long post!