Hi Stephan,
well, hours for 5000 files is indeed too long.
I don't know how your configuration is (HDD, SDD, which Cloud is used, etc.), maybe you can contact us via support(at)boxcryptor.com regarding this.
Please refer to the post here.
A 64bit version isn't planned for the moment.
On the other hand, the 32bit version is compatible with more systems compared to a 64bit one.
Best,
Yasmin