I'm not Reputable enough to upvote or comment yet, but LukeH's answer was spot on for me.
As AES encryption is the standard to use now, it produces a base64 string (at least all the encrypt/decrypt implementations I've seen). This string has a length in multiples of 4 (string.length % 4 = 0)
The strings I was getting contained + and = on the beginning or end, and when you just concatenate that into a URL's querystring, it will look right (for instance, in an email you generate), but when the the link is followed and the .NET page recieves it and puts it into this.Page.Request.QueryString, those special characters will be gone and your string length will not be in a multiple of 4.
As the are special characters at the FRONT of the string (ex: +), as well as = at the end, you can't just add some = to make up the difference as you are altering the cypher text in a way that doesn't match what was actually in the original querystring.
So, wrapping the cypher text with HttpUtility.URLEncode (not HtmlEncode) transforms the non-alphanumeric characters in a way that ensures .NET parses them back into their original state when it is intepreted into the querystring collection.
The good thing is, we only need to do the URLEncode when generating the querystring for the URL. On the incoming side, it's automatically translated back into the original string value.
Here's some example code
string cryptostring = MyAESEncrypt(MySecretString);
string URL = WebFunctions.ToAbsoluteUrl("~/ResetPassword.aspx?RPC=" + HttpUtility.UrlEncode(cryptostring));