Here's what I got from GoodReader support today:
Hi Ken,
Sorry you're having this trouble. Unlike with PDF and TXT files, for which we've written our own viewers, we use iOS's built-in viewing engine for MS Office files. This engine sometimes shows MS Office files incorrectly and in some cases it's not able to open certain MS Office files. Any changes or updates to this behavior would be associated with an iOS update—unfortunately it's currently beyond GoodReader's control.
For all MS Office files, not all parts of those files are embedded into the file itself, the original program may be performing a task to display information in that file. For example, a sum calculation in an Excel document must be executed by Excel—GoodReader does not have the ability to perform that calculation, so you will likely see an empty field in that case.
Currently the best solution would be to convert your MS Office files to PDFs. In this case you will solve the incorrect appearance problem, plus you'll get the ability to use our Find Text in PDF files feature and other PDF-specific features, like PDF Annotations, Highlights and Markups.
Let me know if you need anything else!