Running any web application as root is not advisable!

As you have already figured out, it is a permissions problem. The reason you had to chmod a+x on /root is because no other user, including the user running apache, has rights to the /root directory (it should be private!).

Either serve the application using the web server's user (www-data on debian IIRC) from the /var/www folder or even better, create a completely new user.

Facts and Observations

Let’s analyse the facts:

1. It works with an extension other than typical executable/code extensions like .dll, .exe, etc.
2. It does not work with a different filename
3. It worked just fine with a previous version; only the latest version is having trouble
4. It works just fine in safe-mode
5. Safe-mode disables all non-essential drivers and service
6. It shows no locks or open-handles
7. It says access denied
8. It cannot be moved, opened, copied, etc.

Analysis

Points 1-3 indicates that something about the contents of the file are triggering the problem. This sounds a lot like some sort of anti-virus program throwing a false-positive.

Points 4-6 point to some sort of service or driver that is causing the problem.

Technical

Security software, like anti-virus programs usually have to run at a low-level to avoid letting malware sneak in, so they use drivers and run under the System process. This prevents most programs from being able to detect that a file is locked by the security program (which is why Unlocker could not find any open handles), and even if they can, they only show that System has it open which isn’t very helpful.

Application and Explanation

You said that you had AVG installed at one point, but uninstalled it. Apparently AVG did not uninstall completely (missed a reboot?) and so its drivers was left behind.

So now, whenever you access a file, the driver locks it to scan, but because the rest of the program is gone, there is no way for it prompt you if it thinks the file is suspicious. If the program were still installed, it would show a prompt and ask you want to do (or more likely these days, automatically quarantine/delete the file to “protect” you). Since the program is gone, the driver component sits there waiting, while keeping the file locked.

Since you had uninstalled AVG a while ago, it probably doesn’t have the latest definitions (if any?), so it would not be able to leave the latest version of php5ts.dll alone, and threw a false-positive, thus locking the file with no way of telling it knock it off.

AVG

I don’t know if AVG ever complained about this specific version of php5ts.dll when it first came out, but it doesn’t now.

Also, I don’t know if AVG is known for having a lot of false-positives, though I’m sure I’ve read that about some AV vender; but a cursory check seems to indicate that searching for false positive has at least 33% more hits for AVG than other AV vendors.

Advice for the Future

This problem occurred because AVG did not uninstall completely and left remnants behind. Unfortunately this is an all–too-common problem. In the future, when uninstalling any software be it anti-virus programs, printer drivers/software, etc. always check if the vendor has provided some sort of removal/cleanup tool/utility (try different combinations of words to make sure you find it).

Most security software and printer vendors, as well as some other software firms and hardware manufacturers will have a (usually small) program that you can download and run to wipe out all traces of their software. Unfortunately, this is usually not built into the uninstaller and must be downloaded manually from their site. Sometimes it will be in the normal parts of their site, sometimes it will be buried somewhere in their support forums. (These are usually compiled from bug-reports from people who found left-over files, registry entries, services, etc. that are left behind by the uninstaller, which is why they are separate.)

In your case, you could have (and still should), use the AVG “remover”.

NB: when searching for a cleanup utility for security software, be careful not to mix it up with a virus-removal tool.