Absolutely... trained with my wife on the weekend after her five year layoff of Aikido (children, work commitments, etc.) and I found that almost every time I tried to throw her she resisted with every ounce of strength rather than trying to roll.
Talking to her about the training I think it came down to a lack of confidence in her ability to receive - not unreasonable given the time off the mat.
I wouldn't discount you subconciously wanting to protect your knee injury either. I've found my ukemi being askew post injury as you tend to favour the uninjured limb.
I'd give it some time, work up to it slowly and try to regain your confidence. I believe ukemi is like learning to ride a bike, it will come back of its own accord but you shouldn't expect to ride a pelaton after time off