Damn, I wonder where did the rest of my comment go... Anyway, binary file issues may be a mixture of AOLServer and ACS. I just tried it again, to refresh my memory, and I guess I found a fix, at least for new-file-storage.
The problem is that on brain-dead win platform a binary file should be opened as binary (this has no effect fo "real" OS's). This adding the following string:
fconfigure $file_to_return -translation binary
around line 352 in
/tcl/new-file-storage-defs.tcl seems to fully fix an issue. I've put
a patch into SDM.