a number of ideas:
1:you keep mentioning paps. these have nothing to do with "disease". They are only looking for cancer. They do not test for gonnorrhea,
chlamydia, etc, unless specifically asked for/recommended by her DR. All the tests for STDs are different swabs, they do not use the same sample that they use for the pap smear. The pap smear is to rule out abnormal cells that would lead them to be concerned about cancer. The pap smear does not test for ANY other diseases (except for occasionally HPV, but they only test for that if the cells are abnormal, and you can have HPV without having abnormal cells at the time of the pap)
Has she had tests for gonnorhea or chlamydia? these are becoming much more common in the general population again.
2: maybe she has thick/copious lubrication when she is aroused? Maybe this really is not an issue. especially since you mention that it happens mainly with intercourse
3; yes, if it is yeast (or
bacterial vaginosis) you can be passing it back and forth. This is more common if you are uncircumcised, as yeast and the bacteria that cause vaginosis both like warm, covered, areas, but even if you are circumcised, you could be passing it back and forth.