It sounds like LPEX code may not be being used for the compare. Perhaps Eclipse code, or some other plugin, is performing the compare.
Once you get the compare results, you can right click in the results area, and there is an option to "Ignore White Space" (at least in RDP 8.5.1 there is).
I'm guessing that the settings under General-Compare/Patch and General-Appearance-Colors and Fonts is what controls the compare, not the LPEX settings.
I agree the default compare using default settings could use some polishing, I've just not taken the time to figure it out.
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