BenPrice,
That sucks... but I am sorry either yourself or your IT team failed though. The limitation of Mac client and 20,000 files has been known for some time.
Your options are three.
1. Wait for Microsoft to release the client (and asking here for a update is pointless. They haven't answered here before).
2. Use a program like Beckfish. 100mb folder limit or to remove the limit $20USD.
3. Use another solution.