Version of AE? I've heard of Collect files not working when you move the mouse or use a Wacom tablet, but other than that It's working for me. Please give us more details.
As for the Collect files feature I seldom use it because I have a specific and well defined file structure for every project that I've used and perfected over the years. I can still go back nearly 20 years and re-create projects from all the original source footage and notes. I have not kept all comps up to date and there are plug-ins that I don't use any more or that are not made or supported any more in my older projects, but all of the source footage is there, in folders with documentation installed on hard drives I keep in a safe. I would strongly recommend that you develop a standard folder structure and use it for every client and every job. It will save you headaches in the long run.
If you report back on your system and version info maybe we can help you get Collect files working again.
The version of after effects is CS6.
I work with OS 10.8.5 on a Mac
Is your CS6 up to date. Just tried it on my office computer, OSX 10.9.5 and it works just fine.
Yes it is up to date.
I'm sorry but I'm confused.. Do you work for Adobe ? Or are you an independent contractor ? I have been working for years on After Effects and it is not only me who is having this specific problem, it is my partner as well. I work in a different way to you.. I respect that you have developed a way that works for you but what I do is different and I rely on this function in After Effects to work.
I do not work for Adobe but I also do not have any problems collecting files. The problems that I have seen reported relate to moving the mouse or autosave.