After being on for about 30 minutes, the Laser I&R output looks very different from the output in the manual. The measurements from the machine are accurate but varies a bit. Could this odd output be the issue, or is this level of performance expected?

Results are dependent on

a.) glass structure (glass and spacer sizes),

b.) coating types (transmission on 760 nm wavelength),

c.) user and environmental effects to the results (the cleanness of the glass, vacuum, possible pending of the glass) i.e. the results are dependent on several variables.

Although you can’t directly compare results on different glass types, the device will perform according to the specifications on typical glasses.

Regarding pictures of the Laser I&R test. You can scale the graph from the lower left corner buttons and then you will have the peaks as shown in the manual.