I'll be the first to admit that this is a work in progress and is far from perfect. If you have read the troubleshooting advice and still can't get it to work, you may have found a bug. Please let me know. Here are some of the larger issues that I already know about, as well as any workarounds.
A SWF file cannot just randomly send and receive data from a server that it is not hosted on, so things such as the username block and Cloud Variables will not work. If you want to make a project that relies on these, it usually makes the most sense to host it on the Scratch website.
Due to what seems to be a bug in Google Chrome, if you try to use the converter in incognito mode, you will not be able to save the converted SWF file. Please switch to a non-incognito window or a different browser.
Sometimes a converted project will show a white screen for a few seconds while the project loads, especially if you have a slow connection or your project is very large (larger than about 10 megabytes). The loading is done by the included copy of Scratch, not the converter, so there is nothing I can do about this.
If the dimensions of the converted SWF do not match the ratio that Scratch expects, there will be a white bar on whatever side is "too long". The Scratch stage is a 4:3 ratio, which is not something that I can easily change, and if I did it would mess up everything. Please adjust the dimensions of the SWF file in the converter or (if applicable) the web page that embeds it.
If you try to open the AS files in Notepad, the lines will all appear to be run together. This is because I use a Mac and the files have UNIX line endings. Please use a better text editor, such as WordPad or gedit.
Adobe has changed the security restrictions in Flash Player 23 and onwards. They basically prevent local SWF files (saved on your computer) from being able to use some Loader functions that Scratch needs. This is not a problem that I forsee a solution to any time soon. However, there are several workarounds. You can host your SWF file on a website, or you can convert it to an EXE or macOS APP. This will bypass the security restriction by making the SWF no longer be a local-with-network file. See this page for more info on converting SWF files to standalone executables for your platform.
Most of these problems aren't going to be fixed any time soon, simply because I don't know how to. This is usually because they are caused by limitations in Scratch or other software. I will continue to do research to see if there is anything I can do about them. If you know of any additional workarounds, please contact me.