Welcome to the Doom9 forums, rod93.
First, if you use BD3D2MK3D, please use
the BD3D2MK3D official thread. This one is obsolete and dead since July 2014.
Frame sequential 3D is just like a normal video, without changes in resolution, but there are two times the number of frames (so 47.952 fps instead of 32.976). Therefore, the 1080p resolution is absolutely normal.
FS is usually not well supported by most players. I suggest to try to use Half-SBS or Half-T&B first. If that works, try Full-SBS or Full-T&B. That should work on PC with a good player (but most relatively old hardware players will probably refuse to play the full resolution.) Also, be sure to use the last version of BD3D2MK3D.
[EDIT] The previous post, by rod93, has been posted in the old "Guide to convert BD 3D to 3D Left+Right Stereoscopic and Anaglyph", and moved here by tebasuna51 after a few replies. Hence my request in the beginning of this post.