I'm upgrading from 1.3.9 to 1.3.9sr1. I've got the files uploaded and the paths set correctly and select Upgrade Database. When I get to step 2, I'm asked to select the Current Geeklog Version. 1.3.9 is not on the list. The list only goes as high as 1.3.8.

Is this correct?

Yes.
sr stands for security release. It means that there were some holes, bugs whatever you call it in some files.
So after this is discovered there is usually, or not , a patch release.
All you have to do, if you already have GL 1.3.9 installed, is to replace the affected files.
Do not upgrade, unless there are changes to db. With security releases there aren't usually.

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Geeklog Polish Support Team

Thanks.
Everything seems to be running fine. Just did not want to screw up anything.