Your problems look like a configuration issue of PHP/Webserver rather than DokuWiki.
You didn't respond to repeated questions for logfile information.
Is this because you cant't access them ?
Do you use a hosting company ?
Did you already try to get support from them ?
My guess is you tried, didn't get any, and don't have access to the relevant logs.
Which makes it difficult for you to solve your problem alone, and for others to help you.
Anyway some suggestions:
I don't see important differences between the PHP-Infos, but just the existence of differences is a hint.
The maindomain and the subdomain are handled by different server-processes using different configurations.
This might cause a lot of subtle problems around cookies, caching etc.
It might even be possible that both servers run with different UID and GID, so the cache can't be shared.
Try the following for confirmation:
Install a second DokuWiki instance under a different path, but use the installer for the subdomain.
subdomain.hoster.com/alternative_path/install.php
Then try if you can use the alternative wiki over the maindomain.
My guess: It will be the other way round - The subdomain will work, the maindomain will not.
(BTW This is a good opportunity to check owner,group and permissions of files created by both servers).
If this is the case, you know how to use the subdomain, and that you can't use subdomain and maindomain in parallel.
You have to decide which domain you prefer and install accordingly.
Otherwise you'll run into problems later, even if you solve the current situation.
Just an example: A closed Wiki contains an external link instead of an internal link to itself.
DokuWiki will use different sessions, it will lose the login information (or worse).
If you really need both domains in parallel and don't have access to config and logs, there isn't much you can do ...
A last few ideas:
Get more information with this:
$URL/doku.php?do=check
Do it for both domains (if possible) and check the differences.
I further suspect both accesspaths have different relative path to DocumentRoot.
Not sure it this can be solved.
Take a look here for details:
http://www.dokuwiki.org/tips:farm2
You might play around with the following config-options for a workaround.
basedir (Base Directory)
baseurl (Base URL)
If you don't use webhosting but have total access to your server, take a look at the following PHP-directive:
session.cookie_domain
This might allow to override the default separation between subdomain and maindomain,
depending on operatingsystem, webserver, temperature, humidity and some other conditions ;-)
I don't believe you'll get much more help here unless you provide details about:
The logs, operatingsystem, webserver, PHP ...
There are some companies who offer commercial support:
http://www.wikimatrix.org/consultants/dokuwiki