It appears these issues have less to do with compatibility with these program and more to do with bugs in Boxcryptor over remote drives. Using robocopy (robost file copy) for example, I receive a "Changing file attributes error" during transfers and robocopy will continually retry until successfully transferring -- mitigating the issue. Seems to be a racey access issue on boxcryptors part. Further if I use robocopy to throttle the transfer rates of boxcryptor the issue disappears altogether.
In fact, now that I think about it, this is similar to an issue I sometimes have when using a script I made to compile and bundle some python scripts into an executable (on a local drive). The last operation in the script is to perform a copy/move on a newly created file and it will fail randomly unless I put a sleep of X amount before hand. Seems to be a race condition of some sort.