The concept of uploading a bank-generated data file of any type to a publicly available web server shocked me right out of my early morning stupor. Surely I'm misunderstanding what you're thinking.
Wouldn't it be better to access the mdb file from Perl installed on your local workstation that's off the public net? Even if you are storing other data on the web server that you're using the bank's file to validate or update, you could build your update offline and run it or feed it to the cgi on the web server eh (or download data from the web server to the local machine for processing)? (egads, now I'm starting to wonder about what other data is stored on the web server...)
As for using Perl to read the .mdb file, did you look at DBI's DBD::ODBC driver discussed in the FAQ?