Auto-refreshing should only occur if some other application is changing files in your repository, because SourceTree refreshes in response to events from the operating system. Is there something this is frequently saving files in your repository, triggering the refresh?
You can disable auto-refreshing in SourceTree either for a single repository (Settings on the toolbar, Advanced, disable auto-refresh checkbox), or you can do it globally in Preferences (or Tools > Options on Windows), the same 'Auto-refresh when files change' option.
I don't know why this hasn't worked for you, I've tested disabling auto-refreshing here, both in the repository Settings > Advanced (which just affects one repository) and in Tools > Options (which is global), and it definitely prevents SourceTree from auto-refreshing at all. Refreshing only occurs when you press F5 or perform an action like committing or *after* performing a stage (not during).
Uninstalling and re-installing shouldn't make any difference at all, but please do make sure you're running the latest version (currently 1.0.3).
I'm also having this same issue with SourceTree (2.1) on OS X 10.10.5 (14F1509). If I turn the "Refresh automatically when files change" option to off within preferences the bottom pane containing the lift of files with changes and the selected files contents continues to refresh when the files are changed by another program.
As of today I am still seeing this problem. The only thing running is visual studio but I am not modifying the file. The diff view isn't stable at all for me. Disabling the refresh shouldn't be necessary. It is useful when it works correctly but I can't imagine what is causing the files to change ever 2 or 3 minutes. The sourcetree diff has become nearly useless with the refresh setting on, and even though I like beyond compare I don't want to have to do an external diff in all cases.
I'm using version 184.108.40.206 for windows. By the way, this problem does not happen with Beyond compare. Beyond compare notifies me when it thinks that the file has changed. Therefore I'm sure that the file not being changed.
See the image below. When I clicked off that setting and ran a stop watch for more than 4 minutes I didn't see the problem. I think that default remotes check resets the log history view every X number of minutes or whatever it is set to regardless of any need to refresh. While staring at a diff, the diff view just clears out and the first file within the log history is reselected every so often which seems to correspond to that setting. It doesn't correspond exactly when using a stop watch but it seems to happen within 30 seconds after the x minute mark according to my stop watch. Why would checking default remotes need to reset the diff view?
I've also had this issue on Windows 10 64Bit Version 1709, running sourcetree 220.127.116.11, happens with LibGit2 enabled or disabled, using system git 2.16.1 + git-lfs v2.3.4. The Push Changes checkbox on FileStatus gets enabled/disabled constantly (not checked and unchecked). And when this is happening I can't click the commit button unless I spam it sometimes I get lucky, closing and reopening sourcetree sometimes temporarily fixes the issue, I have auto-refresh off
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