I am running a small account for a client who, over the past year has had 1,000 clicks from Adwords (According to Adwords) But when I look at the Google Analytics for the same timeframe the line under Google CPC - only shows 124 clicks? Anyone else have this issue? or am I reading the analytics wrong?
Yes, a lag time is understandable, but the account has been active for about a year, a lag time of 2-3 hours wouldn't affect 9 months of click data
I have the same problem however we use subdomain for internal tracking. This problem may also occur also if you are using a lot of variables in your landing page URL (id sessions, cookies etc). Did you switch to the new Analytics tracking code or are you still using the old one (urchin)? There may be conflicts there, Google did say they will not update the urchin code and with the new AdWords interface they may have switched entirely to the new one
You're best off speaking to your Google account manager about this to be honest - the linking between adwords and analytics accounts can sometimes go wrong and it is a total pain to sort out unless google get involved