No Tom, you're not losing your mind. This is fairly common problem with not only Seagulls but with really expensive guitars as well. There are a few possible solutions.

The first is to take it to a luthier and have him check the neck angle, intonation, condition of the frets, level of the fingerboard and if need be, replace the saddle with a "compensated" saddle - could be that the scale length of your B string is off just a hair for it to intonate properly and a compensated saddle might just do the trick.

The other suggestion is that tuning all the strings with a tuner only gives you a technically accurate tuning for a given chord. You have to learn to tune the guitar to itself. No guitar will properly intonate on every single chord nor in every chord position up and down the neck. This is the nature of the beast. Get used to tuning the strings to each other, and use a tuner only on the low E string to give you a concert pitch reference.

It could be that your frets are worn down, or, that you are pressing too hard on the strings, or that the fingerboard has developed a slight warp or "bubble". Again, take it to a respected luthier in your area to find out if this is the problem and at least eliminate this as a potential source of the problem, and then look to some of the other suggestions I've mentioned.

Also, depending on where you live, climate changes can produce subtle differences to your intonation due to the bridge area (top) rising and falling ever so slightly depending on the relative humidity or lack of.

There are others here who may be able to add more, or you could send an e-mail to Frank Ford at Frets.Com (but I suspect Frank will more or less reiterate what I've mentioned here.)