Not a problem with the equipment. It's simply that the two recordings were made with different clocks which were not sync'd. When they are played back using the same clock, those differences make the two recordings run at slightly different speeds.*
You'll need to manually sync the two recordings. That can be done in a few different ways. You can do it like you've done, cutting up one recording into shorter segments which are not long enough to notice the drift, and aligning each. Or you can do some calulations and change the sample rate of one slightly to compensate for the timing drift. Or you can use an editor with a 'shrink/stretch' type function which is the easist way to do it. I use Samplitude and it's pretty straight forward to shrink the longer file to match the shorter one by aligning a transient at the begining and very end of the file. I don't use Wavelab but I think has a similar function, I'm sure other editors do as well, not sure if Vegas does, but look into that. Someone will probably chime in who knows if it does.
*Not that it helps you with this, but if you were to play the two recordings on the devices with which they were recorded, manually sync'ing the two at the start, they would stay in very close sync for the entire hour. That's because the files would be played back using the same clocks with which they were recorded and the differences between them wouldn't matter, only the consistency of each clock with itself from recording to playback would matter.