php.ini overrides are not being recognized

*** Post Preamble Apology ***

First of all, my deepest apologies for posting this incorrectly before by reopening the feature request override php.ini as a critical support request.

Frustration and stress can make you do stupid things. I should have remembered the motto of my college chemistry lab instrumentation manager, "Poor planning on your part does not constitute an emergency on my part."

Although this really isn't a matter of planning at all, I realize I should never had labeled the issue as critical support request.

Again, please except my apologies for my poor for netiquette. I realize the errors of my ways, and will not do it again.

*****************************

So again, here is my problem:

I'm not sure what I'm missing or doing wrong, but the changes I made to php.ini files are not being recognized.

Some time ago I made changes to post_max_size, upload_max_filesize, max_execution_time and max_input_time in /opt/etc/php.ini and touched /opt/etc/custom.php.ini and things were working fine until sometime recently when I discovered that all my BOA sites had a limit again of 100MB for uploading files.

Upon investigation I found the feature request override php.ini post and discovered that my changes were not made in /usr/local/lib/php.ini. I don't recall if I ever made the changes here or not, I don't think I did as I don't recall knowing about this file, but regardless the settings for post_max_size and upload_max_filesize were 100MB, so made those changes to the settings and others that I need.

I tried to restart things by running the Barracuda script, but the limits on my site file uploads were still 100MB.
I doubled checked both /opt/etc/php.ini and /usr/local/lib/php.ini and the changes were still saved in both files.

So I restarted my Linode Ubuntu VPS and still all sites still have the limit of 100MB.

I can't figure out what I'm doing wrong or missing. Any suggestions would be most appreciated!!! Of course I discovered this problem while trying to do something that has to be done yesterday, if you know what I mean. (Hence my frustration and stress that caused me to do stupid things this morning.)

Also, I have attached my BOA files from:
/var/aegir/config/includes/barracuda_log.txt
/var/aegir/install.log (password removed)
/root/.barracuda.cnf

Thanks for your help in advance!!
Steve

P.S. From my barracuda_log.txt file you will see that I'm using Aegir HEAD / Barracuda BOA-2.0.3-dev. This because of I was having problems upgrading to BOA-2.0.2. See Upgrade to BOA-2.0.2 failing and git is being removed on Ubuntu Lucid. However, I just discovered a reply there that there was a patched released to fix this against BOA-2.0.2. I have had problems getting notifications from D.O. and hopefully have fixed that (again) today.