The RESTAdaptor.setPositionalParameters method relies on the regular expression ([\\/=:~])(\\?[idvnt]) to find YADA markup in a url string. When the operator is URL encoded, however, this markup is unrecognized (i.e., ignored.)
In some cases, for example with JIRA JQL statements in a url, this causes the request to return a 400 error because, e.g., %3D?v is not replaced with a value like =value but instead is lest as is and throws an error because the ? char is reserved. Obviously the query would fail to return any results in the best case.