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Sometimes Home and Deep may both show the "same" PR. But remembering that PR is really calculated to many decimal places, Deep may be beating Home (5.9485766322 vs 5.0239162743, but they are both PR 5).
There's no reason this PR scenario would harm a site in the SERPs. Deep pages still circulate their high PR back through the site (assuming they have navigation links) and in general, high PR deep pages are helping, and not harming.