A: 

You are basically asking if the MD5 implementation in .Net 1.1 was broken.

I do not think so. I think the problem lies elsewhere.

Sam Saffron
A: 

I don't think the .Net MD5 hash code have changed in VisualStudio 2008.

But I think that:

Return ASCIIEncoding.ASCII.GetString(hashResult)

You are converting binary data to ASCII, and loosing characters, maybe the problem is in a new database driver. And probably you will need to change your stored values and start using a blob field or converting to base64 and using a text field.

Aragorn
A: 

Trying to be more productive than my comment ...

You could try using an independent md5 hashing algorithm to verify the encoding, there are some web based ones or use openssl.

Harald Scheirich