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What version of PLTS are you running? What is the build number?
I am running PLTS 9.3.1 Foundation SP1 Patch1 Build 494. I cannot reproduce your issue.
Other users reported your issue at PLTS 9.3 Foundation Build 1444 which resulted in the following defect:
Defect ID: 33280
Name: Geo on Geo check not saving the tolerance value
Defect ID: 33280 was fixed at PLTS for ArcGIS 9.3 Foundation Patch 1 released 8/22/08.
If you are running PLTS 9.3 Foundation release Build 1444, you should download and install PLTS for ArcGIS 9.3 Foundation Service Pack 1 released 11/18/08 and PLTS for ArcGIS 9.3 Foundation Service Pack 1 GIS Data ReViewer Patch released 5/8/09 from the link below:
This is indeed the case. Thank you Dan!