Here's what I'm thinking on the semen vs. hand cut issues in the Skype conversations. Nothing really new here, but this is how it ties together for me.
1) Rudy knew that he had cut his hand and bled, and that this would be found out by any competent CSI, so he makes up and volunteers an innocent story to cover up: some other guy cut me when I was doing good things.
2) Rudy has read a newspaper article, and knows that CSI is looking at semen. Unbeknownst to Rudy, what the cops are actually looking at are the results of a rape kit, which in fact are negative for semen (as far as we know, not having the full results). Rudy, however, assumes that CSI would have found and are examining the big stain that he left on the pillowcase, right between the dead/dying victim's legs, a stain, which under the circumstances, is impossible to innocently explain. So, prompted for an answer about semen, he has only two choices: 1) admit that the stain was his, an admission that, given the circumstances, is immediately incriminating, or 2) deny that the stain is his, a denial that is self-serving short term and long-term can't really hurt him if subsequently disproved because at that point he's already caught. Turns out for Rudy, that his denial never was disproved, because CSI not only didn't discover the stain that Rudy was worried about, but when it was discovered, CSI peculiarly refused to test it.
So, for me, the difference between the two issues is that the blood is susceptible to a believable (by those among us who are credulous of such things) cover story, whereas there is no innocent explanation for the semen, because it was impossible to concoct a story to establish the innocent presence of semen between the legs of the dead/dying victim. Rudy had nothing to lose by his denial, and short term, maybe felt that he was deflecting.