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I've suddenly got half the click rate, although impressions are about right. Presumably there's a lot of data shifting around at the moment.
I'm not sure what you might be experiencing, but be sure to consider JohnKelly's post above yours. Reported impressions include PSAs and AAs. If the percentage of impressions that are PSA/AAs increases and the CTR of the Adwords ads stays flat, reported CTR will decline since what Google calls CTR isn't actually what I'd consider CTR (or what most would consider CTR to measure) - it's Adwords clicks divided by all impressions (Adwords impressions + PSA impressions + AA impressions).
You have to be running a script to somehow count Alternate Ad impressions in order to do this, though.
To clarify, I don't run PSA's but alternate ads only. This lets me track easily. The formula I use is:
CTR% = Clicks / (Impressions - AltAdImpressions) * 100
Google supplies Clicks and Impressions in the report. You have to supple the AltAdImpressions yourself.