It's the onboard mic. There is also some freezing of the screen (although very short; about less than a second) at the beginning of the tape.
There was this time that the footage has blue horizontal stripes (the same blue color when a camera is in VTR mode), as if the "scanning mechanism" in the alternate field (or whatever it's called) is not working. It happened just once and never again occurred. Although I get a bit worried because it might happen again when shooting a very important event.
I do not know if all these are related to the popping sound, like if they happen because of the tape head or recording mechanism.
Actually you could be experiencing two different issues. I too have an older XL1, bought used, and I haven't taken it in to a Canon dealer to have proper service yet and occasionally I do get mini-DV dropouts. It just might just need a head cleaning.
As for the audio, the XL1 actually samples audio slightly higher than 48 kHz:
Name: Peter Ralph
Date: Nov 30, 2002 at 4:44:25 pm
Subject: Re: Canon Audio Issues
Many Canon DV cameras sample audio at rates slightly higher than the norm (something like 48.0487k instead of 48k) . This can cause sync problems when capturing clips longer than 5 minutes or so. The auto sync compensator built into FCP takes care of this problem - I dont know which other NLEs provide this functionality.
Canons and Macs play well together.
Actually, this info refers to the XL1, the XL1S, XL2, HD1, etc. sample audio at the normal 48k. And he's right...I capture footage from the XL1 on a Mac using Final Cut Pro 5 which automatically compensates for the audio discrepancy...so you might check the settings of your non-linear editor or whatever.