(Please forgive the delay in response. Technical problems prevented the mailing of a number of responses.)

1) The Gemara you remember is in Eruvin 100b.

2) It seems that the above Gemara is referring to a person who did not plan it in advance but changed his mind in between, as the Gemara here in Pesachim says is not a problem.

3) One can also say that this is connected with the Gemara later, on 110b, that says that if someone is not particular about the issue of Zugos, then the damging forces are also not particular to harm him. Since most people are not particular about Zugos nowadays, and the whole topic is not mentioned in the Rambam or Shulchan Aruch, the Gemara in Eruvin gives the advice to have two acts of relations, since for most people this could not cause any harm.

4) Here is another answer to this question that I found in Otzar Mefarshei ha'Talmud on Pesachim 99b (to Rashi DH Tzerachav; pp. 465-466). This is based on the verse, "Shomer Mitzvah Lo Yeida Davar Ra" -- "one who keeps a Mitzvah will not know of a bad thing" (Koheles 8:5), from which we learn that one does not come to misfortune by doing a Mitzvah.

Accordingly, since it is a Mitzvah to have Zachar children, it follows that the danger of Zugos discussed in the Gemara does not apply.

5) However, this answer seems to be contradicted by the question of the Gemara itself (99b) that asks, how could the Rabanan institute the drinking of four cups of wine at the Seder, if they comprise Zugos? Since it is a Mitzvah to drink the cups on Seder night, there should be no danger involved in doing so!

6) The Otzar Mefarshei ha'Talmud cites commentaries that answer based on the explanation of the Ikarei ha'Das 14:2 (printed at the end of many editions of the Shulchan Aruch, YD part 3), who discusses at length the question of whether the principle of "Shomer Mitzvah Lo Yeida Davar Ra" applies to things which are forbidden because of danger. He writes (DH HD'T) that there is no proof from the question of the Gemara here that there is a danger even where there is a Mitzvah, because the Gemara means to say that since it would have been possible to institute five cups, this surely would have been preferable, because this way one would perform the Mitzvah and also avoid any danger. When it is possible to do the Mitzvah without any danger, this is clearly preferable than relying on "Shomer Mitzvah Lo Yeida Davar Ra."

When, however, it is not possible to do the Mitzvah without relying on "Shomer Mitzvah Lo Yeida Davar Ra," then it is safe to rely on this principle. Since having two acts is the only way of increasing the likelihood of having a Ben Zachar, it follows that there is no danger in two acts.

Kol Tuv,

Dovid Bloom