How does "does not boot" look like ? What happens exactly ?
AExplorer has nothing to do with the boot process. Different versions are interchangable. I doubt it has anything to do with running different versions on Amiga and PC.
The only thing I could imagine is that you copied AExplorer to WBStartup and forgot to set the DONOTWAIT tooltype. Or you added AExplorer to startup-sequence or user-startup without "run" in front of it.
Another possibility is that you tried to write something onto your hdd's hdf through the AmigaExplorer window. This would indeed destroy all data on that partition. But I doubt that, too. First you have to give more details.
Bye,
Thomas