Rain
What I could best describe as fatigue has caused me to hear bass frequencies out of tune on occasions. If I keep at it, it only gets worst.
 
Working with headphones will almost inevitably mess with my perception of bass after a while. And it's like one of those hidden image thingies - once I've heard it out of tune, it's all I can ear - the only cure is a break, and listening to something else for a while.
 
The sensation is quite weird actually, because your reference keeps drifting - almost like being dizzy or feeling seasick.

Happens to me too. It can be scary if I have to drive right after a long session.
 
Regards,
Dan
 

I use Scarbee just to compose a rough idea of the bass lines for my songs. That track is almost always replaced by my Fender modified Jazz Bass which is fretless so I know that it is laughable that any instrument would play perfectly in tune for any length of time.
I'm glad you found the problem. Ear fatigue and tinnitus are always lurking in the shadows to come out and bite us at anytime. When you're under a deadline you have to just hope for the best if the pressures on. Otherwise, the only remedy is shorter listening sessions. If at all possible, I never track, mix and master in the same day! That break also gives you some time to re-energize your enthusiasm about the project. And I try to accomplish what I need to as quickly as possible. And needless to say, at a reasonable volume level. If you find yourself reaching for the volume knob to turn it up more and more and constantly re-adjusting the EQ, that is a sure sign that ear fatigue is setting in and anything else you try to do is pretty much shooting yourself in the foot as far as your hearing is concerned. These are just a few of the things I have found that helps my hearing. Hope there is something in here that helps.
BTW, I often wonder how many guys that own cars with 5,000 watt stereo systems are walking around constantly responding "Huh?"

Bass notes often sound out of tune when played in solo mode.. I noticed the same thing with Jay and Pre bass but once I play it back with all other instruments, it sounds fine..

Thanks! Felt better knowing it's a common fatigue issue.
 
I've this experience as well (not related to out of tune, rather out of key) - I would experiment with some odd chord progressions with key changes cutting in and after jamming / recording riffs over the odd changes.. sounded right. Then next day with a fresh mind and not recalling what I've did, listening over for the first time - I'll go.. what is this ?!! it doesn't make sense. But after a few round of listening, it felt right once more.

Hey, you may have invented a new art form! "Jazz for people with tired ears!" LOL