Unable to save any hours worked

It was expected : see step 2 (you must change some server parameters)

This is due to limitations in the number of variables posted on the form.
PHP V5.3.9 introduces this new limitation (but it may have existed before through suhosin) to 1000 vars in a form.
All the applicative imporvements have been done to limit number of variables.
Then, either you succed to change the settings.
Either you must take car to limit the number of lines of assignement for one resource.
(maybe the project breakdown is much too detailed).

Where do you get this alert ?
(a print screen ?)

We have done that

Done what exactly ?

and now we are getting this alerts:
$user->id,'readFlag'=>'0', 'idle'=>'0'); $alert=new Alert(); $lst=$alert->getSqlElementsFromCriteria($crit, false, null, 'id asc'); if (count($lst)==0) { return; } $date=date('Y-m-d H:i:s'); foreach($lst as $alert) { if ($alert->alertDateTime<=$date) { echo '' . htmlEncode($alert->title) . ''; echo '
'; echo $alert->message; echo ''; echo ''; return; } }

I d'ont understand what you mean : this is some PHP code, you should never see this on your screen.

check what you did, you probably broke some php configuration.