Photoshop not allowing me to save as jpg

Original files are in jpg, I stitch them up into a nice pano and the only format it will allow me to save it in is a massive tif file.

It's in 8 bit and I've tried flattening the layers, from the tif file which I saved and reopened.

JPEG has to be a flat, single layer file, but PS should perform that flattening as a part of the Save As process. Just how many pixels wide is the pano? It may be that you've hit a size limit. I did a quick search and hit upon this thread, which seems to state that there may be a limit of 32K or 64K pixels on the long side of a JPEG. And wikipedia seems to bear this out.

Is there a file size limit for .jpgs?: Retouching Forum: Digital Photography Review

It is a big file, 31292 x 4.5k to be precise. It allowed me to save as a png after a crop and then a squish down to about 1500 x 4.5, and it took about 5 minutes to save.

I'm assuming you're using PS CC 2014, right? Or is it an earlier version? You're near a 32K pixel limit with the original file, but it should still save it from all I can find. Have you tried using the Save For Web function?

Image > Mode > RGB Color

Make sure you're using a JPEG-supported format. For example, you can't save Indexed Color as JPEG.