Sorry, I don't know how to solve it. Best way is backup and made partitioning from scratch.
In any case, it is a good idea to use for partitioning only disk tools from one operation system on single disk (or better one tool only).
In the past, I had problems even with mixing tools from Linux and MacOSX on one HDD.
Also on Pegasos 2 mixing HDconfig and MediaToolbox produces some warnings.
AmigaOS3: Amiga 1200
AmigaOS4: Micro A1-C, AmigaOne XE, Pegasos II, Sam440ep, Sam440ep-flex, AmigaOneX1000
MorphOS: Efika 5200b, Pegasos I, Pegasos II, Powerbook G4, Mac Mini, iMac G5, Powermac G5 Quad