It's been quite a long while after you posted this question, but fact is even it's 2018 now, I still encounter the same issue.
However, I found a walk around for the issue (my version is QlikView 12), explained below:
[Field] from [QVD] being filtered using [WHERE] clause being won't work unless the filed is renamed, with a name different from the one you STORE into the QVD.
For example, I have below script, and in this case, after I renamed the RegionShortName to RegionShortCode, the WHERE Clause will work. (if not renamed, the two commented out WHERE clauses both won't work)