same with me (2 x win7 pro x64 pc & Notebook)
test this version
i can run portable programms inside boxcryptor without crashes and file corruption.(ssd,usb,lan tested)
all later versions do with me these problems.
programm crashes destroy config files in different time.(chrome portable,tor portable,skype portable,...)
i know this version have another bugs fixed by the next versions.
v1.5.403.131 is last version works for me.
"I had previously been using TrueCrypt for my home directory without these problems."
same here :)