I have not used that exact scanner, but have had quite a bit of experience with CT/DC values and the GRE scanners.
My first thought was wondering if you *need* to use the CT/DC values. If there is an agency on the same frequency that you also receive, then I'd agree you need them programmed. Otherwise, I usually set a channel to CT/DC .. search and let it display a value, but not require it to open the squelch.
My second thought has to do with how you have your squelch knob set. You should make sure that your squelch would not be open if you were parked on a channel set to FM. Since both of your channels are using this decoding, you COULD run your squelch fully counter-clockwise, but that will actually slow down the entire process.
When I compare how all of the scanners I do use decode CT/DC values, some scanners are clearly SLOWER than others. The oldest scanner I have which performs this function, the PRO-92, is clearly the slowest of what I have.
The analog scanners use a dedicated IC to perform this function, and it requires time to determine the frequency. I could see that if you are changing modes (one channel is CT and the other DC) that it would slow it down. From what I've seen, the digital scanners use a function in their DSP to perform this function, it is much more elegant (faster). While I don't expect you to have to get a digital scanner to get faster CT/DC decoding, I'd bet the PSR-300 is faster than the 200 from what you're saying (at least the way I operate mine).