Two problems I have had:
1. E-ticket to Egypt - got there OK but upon return, flying in on Jordan, transit Egypt. NO! Customs and Immigration would not let us into Transit Lounge - had to pay $15 each for visas. TWA has still not reimbursed us.
2. Same time - 3/99 - daughter flew e-ticket on Alaska, SJC to Bend, OR. Wanted miles on TWA, called Alaska, got her # in, NO Miles, neither airline will even talk to me. Have boarding passes with ticket number. Customer service dead both places.
Have e-tix now to PHX with UAL. Have not had trouble with them before. Here's hoping.