The databases are different.
First, go online with the non-matching filename, and then do a save, and answer yes when prompted to upload everything.
Then do a Tools > Compare and compare the two whole projects. That will point out differences in the I/O config, processor settings, and there should be no differences in the ladder logic.
Next, do an Ascii database (*.csv format) export of both RSLogix files, and you'll probably find out that one of them has more documentation. The other may have been truncated automatically or manually, or cleaned up by deleting spare stuff.
You can compare the data bases side by side and find out exactly. You can do this within RSLogix, but I prefer to open the *.csv files in Excel so I can do a better job of sorting and searching for differences.
The only area of documentation I don't know how to export is the I/O config data. That stuff impacts offline file size, but you'll have to compare those details using the compare utility within RSLogix or by manually checking through all the screens for differences.
Note that each address can have multiple database entries, but you may only see one of them while viewing the ladder. There is the (most commonly used) address comment, and also instruction comments. One address can be described with completely separate bits of text depending on how it'd used in the ladder program.
For example, you can call XIC B3:0/0 "Auto Mode" and XIO B3:0/0 "Manual Mode". If the program contains no instances of the XIO B3/0 address, you'll never know that you are using a few bytes to describe it that way.
I usually try to eliminate instruction comments because they can confuse the reader, and just stick to address comments that will appear the same for any instruction that references them. When I read XIO "Auto" I am thinking "When not in auto, then the rest of the rung will happen...".
Another area that can lead to extra database entries and confusion: Timers and Counters comments: I try to only comment the main element name, not each and every bit and sub-element. If T4:0 is "E-Stop Dwell", all references to its bits will get that same label, and I don't really want to see them described differently in most cases.
Of course, RSLogix will prompt you when entering XIC T4:0/Dn to add a comment, but I just skip it.
I will delete those extra descriptions when I find them too. The built in bit descriptors (like EN, and DN) in conjunction with the base element description are plenty for me to understand the code.
Also, it is easy to end up with stray unnassigned rung comments. You can open those up within RSLogix and delete the ones that have no address or file/rung assignment.
In the left pane, scroll down and dbl click to open the various database icons. You can find dead end rung comments, address instruction comments, and address comments there that will affect file size.
At certain times, RSLogix will prompt you to clean up the database and will elminate the unused addresses and their comments. It doesn't always do a thorough job. I prefer to always answer no to this question, because sometimes there are commented addresses that aren't used YET. I don't want to blow away those comments, or the ones for I/O that are actually wired but not currently in use. That is information I want to keep, but other technicians may not realize that and may answer yes to the prompt because it "seems like a good idea" to them to keep things "cleaned up".
Lastly, when RSLogix "zips" up it's "project file package" before saving, it probably does some housekeeping and orgranizng, maybe leaves some padded space here and there, that may explain why a program with just a few additional comments or rungs is several kbytes larger than another.