I think they had feelings for one another. But nothing ever happened. It was like she told Jaffen at the end of Work Force - it wouldn't be appropriate for her to "fraternize" with a member of her crew.
Well, in fact, that was Jaffen who clearly said it, even if Janeway had let him hear a few seconds before.
JAFFEN: I can see why you'd rather live here.
JANEWAY: I'd offer you a position. I could always use another skilled Engineer. But as the captain, it wouldn't really be appropriate for me to
JAFFEN: Fraternise with a member of your crew. Well, at least my memories weren't tampered with. According to the medical reports, I really did come to Quarra looking for a better life. And now that I've been promoted, I guess I've succeeded.
JANEWAY: Promotion?
JAFFEN: They had to replace our shift supervisor. Something about acquiring workers illegally.
JANEWAY: Congratulations. You deserve it.
JAFFEN: I thought you might like these back, to remind you of our time together.
JANEWAY: I won't need souvenirs to remember you.
(They embrace.)
I'd say that:
- the big difference between what happened between Capt Janeway became later only Kathryn after the ion storm/ Chakotay on New Earth and Kathryn 2.0/Jaffen on the modern planet, was where the first did not consume the romantic relationship feelings which was appearing slowly but surely (without the discovery of the serum, the two would have ended up a life à la Adam & Eva, without a doubt but it would surely have taken time, mainly from Janeway), the second quickly fell for each other to the point of deciding to live together as a couple, what included having sexual intercourse, of course but even brainwashed* when she met and lived with Jaffen, the love story she shared with her alien lover was true and not one straight out of her mind, easily erasable after a surgery and besides, proof of this is, once back on Voyager and after to have been treated by the Doctor, the memory of Jaffen had not disappeared, any more than her feelings for him! And it would have been easy to fall in love with him again.
- the common point Jaffen would have shared with Chakotay if Jaffen has accepted a position on Voyager, he would have automatically become a subordinate with whom the Captain could not carry out (Chakotay) or continue (Jaffen) an intimate relationship. At least, we cannot reproach to Janeway to put her happiness to the forefront, no matter the circonstances.
* IMHO, I think that our Kathryn Janeway isn't so different from the Kathryn Janeway we saw/discovered on this planet, a sparkling woman full of life, impulsive and funny ..., once she accepts to be stripped of her Captain mask but I guess that after 7 years where she was forced to wear it round the clock or almost, the mask had to stick to the skin to the point of not being able to detach herself from it and the duties the mask inspires.
-> Mark and somehow, Chakotay (when they were on New Earth) had to know the free spirit Kathryn and even if they were already in love with her, they could only fall harder thereafter... ,
-> Maybe I see too much but in making the decision to stay on the modern planet, Jaffen wouldn't decided to "sacrifice" himself for love in order not to become a burden for the woman he fell hard, who, wouldn't have been able to focus 100% on her command and her mission to bring her crew safe at home?!
-> In short, it was easier to keep working side by side with Chakotay after New Earth, because nothing serious had happened between them while with Jaffen, what had happened on the modern planet would stuck in their mind/memory which would eventually disturb and prevent them from working together.
