Hi Liz,
Happy to help with any questions you may have about StarTools, or recommend other software.
ST is meant for astrophotographical specific post-processing, with an emphasis on fixing common beginners' problems and protecting them from bad (destructive) decisions. For all your other needs, there is some great software available for free that does the pre-processing such as stacking and alignment (Deep Sky Stacker, Registax, AVIStack).
If you're looking for a nice all-in-one solution that also doesn't break the bank, also have a look at Stark Labs' Nebulosity. Its post-processing side is a bit more basic though.
It must be said that if you're shooting in JPEG, you're not doing yourself any favors when doing astrophotography. This is especially true if you're only doing single exposures.
A JPEG image only stores 256 levels of brightness (it is said to have a 8-bit depth), ranging from 0 (dark) to 255 (white). As you know, the nature of most interesting objects in space is that they're very very faint when viewed from earth. This means that the interesting stuff in your picture always sits in the 'very faint' region in your JPEG (let's say brightness levels 0-15).
It's the job of the post-processing software to pump up those brightness levels to something we can see and admire.
The trouble is that having only a few distinct (16 in our example) brightness levels to work with, is really not enough for any software to work with and create a nice image from.
What you'll want is having your data recorded in a 'higher-bit-depth' format (such as a TIFF or FITS) that stores more than just 256 brightness levels - let's say 65536 (the latter corresponding to a 16-bit depth). In that case the very faint stuff in our example sit in the range of 0-4095. Now we have 4096 distinct brightness levels to work with - this should be enough for any software to use.
Also note that converting your JPEG to another format will unfortunately not help things. The 256 distinct brightness levels will just be spread over the new range (let's say 0-65536) in such a way that they will be evenly spaced. E.g. 0 becomes 0, 1 becomes 256, 2 becomes 512, 3 becomes 768, 4 becomes 1024, and so forth. The brightness levels between 0 and 256, 256 and 512, 512 and 768, etc. will simply not be used, so unfortunately you're not gaining anything.
To make a long story short, this is why using 8-bit images (such as JPEG) for astrophotography is a bad idea. It is also the reason why StarTools does not import JPEGs - it is to discourage beginners from accidentally using them, as they will lead to bad results.
Again, happy to help!
Cheers,