GMaptool and gmt are compressed with UPX. This is GPL program with source code avaliable at Unfortunately many virus scanners are unable to scan compressed exe and give warning when detecting compression.

All results generated by VIRUS TOTAL.

Scan resutls form 14.11.2012:
If your scanner gives viruses warning, download UPX and  decompres GMapTool.exe and gmt.exe. Then check again.