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I have tried those settings and it now completes after about 5 minutes but has found no files differences and no report generated. This seems strange since I have as I said updated several modules, the Akeeba backup etc and these have always been reported as changes in earlier releases.

This is indeed strange. Please take a look at the Configure page. Please put the following in the "File types to be scanned" text box:

php
phps
php3
inc

You should only put the extensions, without a dot or a star, in there. Normally the field should be pre-populated with these settings.

Again it just runs and runs even with the suggested settings.

Look, it took 5 minutes to scan no file whatsoever (since you were using invalid settings)! This tells me that actually scanning something will take hours.

It has always run successfully prior to this last release, and I have never had cause to change any of the settings from the default.

This is because there were no settings to change. If it crashed, tough luck, there was no way to fix it.

The 'No report generated' might be true IF it somehow in the earlier runs created its list which I never saw of course, since I terminated it after 30 mins of running.  In which case I could re-install something to test it again ot would 'touching' a file be sufficient?

No. You seemed to have used invalid settings which is why nothing was found. No files were scanned. It just took 5 minutes for the code to walk through your site's files/folders structure.

Re: the progress bar in the clean temp directory, in previous versions the bar has always been shown, even when there is little (or nothing) to clean, yet I have not seen it in the current version at all.  Is this one of the changes?

No. The code was actually not even touched since several versions ago. The progress bar appearing depends on how much cruft there is the tmp folder and how long it takes to delete it. If takes less than 3 seconds then no progress is shown, ever. That has been the case ever since version 1.0 :)

One other thing I have noticed is that in the ticket notification message I get a number of caret A characters. i.e.  This messages subject was:

Yes, I know! I'm trying to iron out main issues in the ticket system. It looks like something in the HTML source is not parsed correctly by PHPMailer. I am actually working on it.

This is probably an ATS problem of course.  [I have seen similar problems on my own site when saving articles etc but have never decided whether it is the editor I am using (JCE) or something else.]

Thanks! You saved me from lots of wasted hours. My test environment uses vanilla TinyMCE, whereas this site uses JCE with a custom front-end profile (admitedly more secure and more sexy than plain vanilla TinyMCE). I now know how to reproduce those issues.

Drat!

After 15 miniutes it has finished AND generated a report.

So it seems like one has to specify 'php' in the file types to be scanned.  Is that expected?

Ha ha! As I was typing my reply this reply of yours came in. I had guessed half an hour, it was 15 minutes. I love it when I'm too pessimistic in my educated guesses! :D

BTW, excluded directories and excluded files can be left blank – unless you have a reason to want to skip certain files / folders (e.g. cache directories and stuff).

The speed should not be affected at all. The settings are read only once, when the scan starts, and kept in the cache until it completes. The settings work exactly like in Akeeba Backup. In fact, the PHP File Change Scanner is Akeeba Engine with a custom archiver engine. Instead of producing archives it simply scans the files. I like reusing and repurposing my code instead of reinventing the wheel :)

The extra file types have to be entered one per line, no commas, dots or anything else.

The excluded directories need not specify the tmp directory or the cache directories. These are always and automatically excluded (otherwise you'd get memory outage / timeout errors). You can enter one directory per line. All folders and files are relative to Joomla!'s root.

I may seem to be pedantic but I suspect that this is likely to be a common question.

I will document all of that, of course :)

You're welcome! Hopefully I will have some time today to look into the email issue :)