Thanks for reporting these bugs.
The first one is indeed a serious one. In PHI, I modify Mathematica's Conjugate to have it expand a bit more than the default, but I seem to have assumed any exponent would be real. Not good.
The second one is also a bug. ComplexConjugate is simplistic and assumes anything not containing an explicit I (Complex) is real. But it used NumberQ to check for this. Also not good.
Both have been fixed in CVS and the fixes will be part of the next release.
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