>> ... before the tech touched the front control panel, the text had lined up for a long time, so something happened when the tech was in the control panel ...
The only setting which would appear to be relevant is the Text Length setting; changing this would effectively change the default line spacing value, and the default top margin setting is probably set to a (small) multiple of this lines-per-inch vertical spacing setting.
>> ... the first page prints out acceptable (not perfect) but then the next two will shift the text up almost half a character and seems to stay there ...
This seems to suggest that your application and/or printer driver is not sending full printer initialisation sequences at the start of the print job, so (at least for the first page marking primitives) the position is dependent upon the underlying printer front panel defaults.
It is never a good idea to rely on such defaults, unless the printer is only ever used to print one document format.
We could check which control commands are being sent to the printer by reprinting a (small (but at least two page), sanitised data) sample file, but selecting the 'print to file' option inthe Print dialogue (or equivalent), then analysing the resultant captured .prn file.
You can perform this analysis using the PRN File Analyse tool in the PCL Paraphernalia application, available via http://www.pclparaphernalia.eu