Is there an easy method for detecting or marking the actual sample frequency? Some time ago, I did a project where the solo guitarist was sitting in a different location. I uploaded rough down mixes to guitarist, who would load the files into his DAW software, record his guitar parts to separate tracks and send the guitar tracks back to me. It worked really well save for one thing: His tracks always seemed a teeny tiny bit off key. Not only that, but he also seemed to drift very slightly tempo wise. The drift became more noticeable on longer takes and that's where it occurred to me that perhaps his and my sampling frequencies were not in sync. After a little trial and error I was able to identify the drift between our sampling rates and subsequently, I would always resample his submissions to get the tracks in tune and sync with my tracks.

Edit: To be clear, the files were sampled at 44.1KHz at both ends. An example: One file is two minutes long. At the beginning of the file, the transient of the guitarists strum is right on top of my drums and bass. But over the course of 2 minutes, the strum consistently lags behind a little further each time. I know is isn't because my guitarist can't keep time--it's too consistent for that.  Looking at the last strum, about two minutes into the song, I see the transient of the drum and the guitar is now 200 milliseconds apart. There are supposed to be 44,100 samples every second so that's a lag of 8820 samples.  A two minute sample at 44,100Hz is 120*44,100 = 5,292,000 samples so relatively speaking, the lag is less than .17 percent. All things considered that might sound like a pretty good tolerance, but a .17 percent drift after two minutes is 200 milliseconds and very clearly audible.

I know that you can use external clock sources to sync up digital streams, but we didn't have that kind of equipment at our disposal. Besides, although two external clock sources would probably be spot on 44.1/84/96KHz, we'd still have to make sure.

In movie and video production, it is common to use a so-called clapperboard to annotate each take, and to synchronize image and sound. I wonder if maybe marking each take with a reference signal could perhaps help identify equipment that's not sampling the signal at exactly 44.1/48/96KHz. I know I could just add, say, a 1000 HZ square signal at the beginning of each take, but then I would manually have to look at the waveform to see if it is spot on. Are there better ways to deal with this kind of problem?

Is it a common problem or just a case of really bad hardware on my and/or the guitarists side?
What file format are you passing back and forth?  The sample rate is stored in the file.  No need for a reference tone.

One of you is likely recording at a different sample rate than the other.  Probably one is recording at 44.1kHz, and the other 48kHz, or 88.2/96, etc.

Now, audio interfaces do vary in sample rate frequency.  44,100Hz can be 44,099Hz on one, and 44,0102Hz on another.  This won't throw your tuning off by any perceptible amount.  Given enough time, you can start hearing a difference.  However, if you are recording against a track already recorded, this isn't an issue.  The playback sample rate on his DAW while recording will be the same rate as the record rate.

So, if you put together a few parts and send him the files, and then he records a couple tracks and sends you the files, there should be no issue here.