Oh crud! Sorry it is clicking again. If you have the correct tone, and the scanner is of good design, you shouldn't miss more than a piece of a syllable over what you would normally miss when in scan mode. PL is one of the best things to be added to conventional scanners ever, IMHO. They allow for eliminating so many sources of unwanted noise and breaks of the squelch.
I can't imagine why the clicking would have a PL encoded into it unless there may be a malfunction with the repeater or someone is playing with the repeater, kerchunking it. I cannot imagine anyone kerchunking a repeater for several hours each day, though. Some of the non-Moto trunking systems will key up on the voice channels on a regular basis, similar to what you describe, but they do this all day, every day. Also, AFAIK, they don't encode a PL when set up like this.
Anyone else have any ideas?
Also, what part of the country are you in and what is the frequency? We may be able to get a clue from that info.
Oh yeah, regarding your question on the tones, they are encoded continuously as long as the repeater, base, mobile, or ht, is transmitting. If your scanner happens to hit a PL'd channel where you have the tone set, it will stop and begin picking up the transmission, same as it would if you were not using PL.