I am having a very similar issue with flexviewer 3.6 and ArcGIS Server 10.2. I recently upgraded a test server to version 10.3 and tested this by pointing the print service to the 10.3 version but I am still getting an issue where the extent at which I print differs from the print page that is created. Typically I am zoomed into a scale of 1128 and click the print button and the page that is created zooms out one scale to 2257 where my addresses labels are turned off.
Here is the initial scale at level 1128 without the option to print at this scale
(InitialScale.png)
The resulting print page zooms out one level to 2257 which my address label are turned off at
(PrintPage.png)
With the option checked to print at set scale and 1128 entered the resulting image appears to be taken at 564 versus 1128
(PrintPageSetScale.png)
I was hoping the jump to 10.3 would rectify this but it appears it does not. Has anyone found a work around or fix for this?
Thank you,
Chris