UPDATE! I found a strange issue with a few levels that causes this tool to report an incorrect (and really huge) number of screens on them. The best example of this is egomassive's Customnibus, which reports a whopping 7970 screens despite having only 4 filled rooms. Apparently, there's an undiscovered bug in the original KS level editor that causes some levels to have their Map.bin file filled with useless null data, which increases the uncompressed map file size by A LOT (about ~30MB in some cases!). If you use this tool on your own level and get an unexpectedly large number of screens (i.e, more than 1000 in a small level), it's very likely that your level is affected and has a big chunk of null data inside the Map.bin file.
This is basically harmless and won't prevent you from playing those levels and/or keep editing them, so you can just ignore it. Also, the GZ compression that KS uses for the Map.bin file pretty much cancels the increase in data size, which is why you don't end with a +30MB level folder and probably never notice this is happening internally. However, while this doesn't damage the actual level data in any way, some third party tools (like this screen-counting tool and KSLC) will report incorrect values and/or have trouble opening these levels. I'm thinking of updating this tool and including a simple check that will detect this error and ask you if you want to generate a fixed Map.bin file. I could also produce a standalone small tool just for that.
Edit: Just to be completely clear, this is not something caused by this tool :P2 If you get an incorrect (and absurdly high) number of screens when using the program on a level, it means the Map.bin file *already* had this issue from the start.
No, I never added that feature since there seemed to be no demand for it and the impact of the filler data on KS' performance is pretty much negligible most of the time (you can shorten the initial loading time by about 1 second in some cases, but that's about it). However, you can do this yourself if you have a hex editor:
NOTE: before you start, remember to make a backup of the Map.bin file, especially if it's your own level!
1) Get any file archiver tool that supports GZIP (e.g. 7-Zip). Alternatively, you can just use the GZIP command line tool if you have that.
2) Rename the map.bin file to map.bin.gz
3) Extract/decompress the map.bin.gz file. This should produce an uncompressed Map.bin file.
4) Open that file in any hex/binary editor program (e.g. Frhed).
5) The map.bin file should start with a set of X-Y coordinates (usually x1000y1000). If that's not the case, then the map.bin file contains filler/garbage data. To remove it, locate the actual start of the map data (try using the search function and search for "x1000" or something like that). Then, select everything from that offset to the beginning of the file (which will be basically a lot of 00 bytes) and delete the entire block.
WARNING: Make sure there are only "00" bytes (check at least one or two pages up) before the x####y#### string. Otherwise you'll be deleting actual map data and you really don't want that. Also, be careful not to delete the "x" character at the start of the string.
6) Save and recompress Map.bin into a GZIP file (make sure you select the "gzip" compression method instead of the default LZMA if you're using 7-Zip)
7) Rename that GZIP file to Map.bin again.
Alternatively, if you only want to fix a single specific level, PM me a link to it and I'll do it for you.