First, you shouldn't need to use a BEGIN block to set the SYBASE env. variable - this needs to be set correctly before DBD::Sybase gets loaded, but in the case of DBI it doesn't get loaded until the first DBI->connect() call.

Now there may be some other stuff going on, though.
I'd take a quick look at the Sybase.pm file and see if there isn't something in there that overrides the SYBASE env. variable (there shouldn't be, but it doesn't hurt to look...)

Michael