I ran into the same problem you encountered when I tried to programmatically disable taptoggle using fixedtoolbar ({tapToggle: false});
I got lucky using the data-tap-toggle = "false" tag in my headers instead of completely disabling taptoggle. Although it might take another job adding data-tap-toggle = "false", at least it works!
I found this question, trying to figure it out myself, and decided to try it. I found the information here: http://jquerymobile.com/test/docs/toolbars/bars-fixed-options.html
The documentation says this in the switch section: this option also appears as a data attribute: data-tap-toggle = "true". I decided to set it to false and it solved my problem. No more taptouch and no longer overlapping! Most of my headers now look something like this:
<div data-role="header" data-id="jqmheader" data-position="fixed" data-tap-toggle="false">
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