the slower upload speeds could be related to Dropbox' deduplication feature. Dropbox brakes up files into blocks and generates a hash (mathematical computation on the contents) of each block. If a block with the same hash already exists on Dropbox' servers (e.g. because another user already uploaded this block before), the block is skipped and not being uploaded again. See also http://forums.dropbox.com/topic.php?id=20925#post-132860
That's why you can copy a large file (e.g. a Linux ISO image) to your Dropbox and it is instantly synced. It saves Dropbox a lot of storage and the users don't have to upload so much.
Now, when you encrypt a file with BoxCryptor, the content of the encrypted file is completely "randomized" and totally diverse from any other file. Even if two BoxCryptor users have encrypted the same plaintext file, their encrypted files are totally different because they were encrypted with different keys.
It's impossible that Dropbox has already stored a block of your encrypted file and all blocks of each encrypted file have to be uploaded - and it might feel slower.