The problem with emu and rotation is, that they compared the angle to 240, not 270 degree 
And whoever made the lnx images, might not have noticed that the rotation flag must be either 0,90,180,270, and not 0,1
... and ...
often enough lnx files are plain rom dumps without any header (thanks to archive). So ... what do you expect? that the emulation checks each rom by hash andcomes with a embedded database? possible for lynx with teh tremendous amount of games, sure.
Well 240 vs 270 is an easy enough fix.
You really have 3 states based on the v1 header -- no rotation, rotate right 90 degrees, rotate left 90 degrees. Just need to map that, and then map the controller inputs accordingly as well.
As to the LNX headers being incorrect...
Im wein ist Wahrheit... (oder Weisheit?)
UGH!
I was hoping that would not be the case.
We've considered writing a little command line tool to dump the headers and check them out. I guess we need to do that.
And if you were to do a hash and a database, is the hash on the whole file, or on the ROM portion of the file? Or both? 
With 100-200 titles, I think that is manageable, even if you had to do it by hand.
I've also considered that it could be time to implement a v2 of the LNX header... Include more meta-data...
The other option (we are more likely to do) is to have all the meta-data in a parallel .json file and/or pull from a server database we maintain.
We'd like to have developer, publisher, release date, screen shots, speed-runs, etc as part of the meta-data.
Feel free to PM/email me if you'd like to take this offline.