Hi,
I've recently upgraded a moodle site from 1.9.9 to 2.3.1+, via 2.2.4. The site is now running on 2.3.1+, but a few issues have arisen during the upgrade. I have been working with my hosting company Hostgator who have been extremely helpful in assisting to resolve these issues, but these last couple are beyond their reach, so they suggested I seek assistance here.
My main issue is that the moodledata folder and file contents are not accessible as expected.
Another issue that exists in one of my courses, is that the add activity button appears like this. 
When I go to the source URL for the image (http://moodle.babymassage.net.au/theme/image.php/standard/core/1345337499/t/add), it displays fine. It also displays fine in other courses.
Also, when I go to 'my private files' in the file picker, it won't allow me to upload anything. When I go to manage, I am sent to a URL that never seems to load, appearing like this;
Some information from the Hostgator technician that may be of relevance is;
Well after working with one of our upper tier administrators on the issues that the image files not showing properly. It would appear that there is a "mapping" issue for the files located in the following folder:
home/heidi/moodledata/5/
For some reason your Moodle installation is not calling that directory correctly and in fact we cannot see your Moodle installation even referencing that folder when attempting to add files from it to your website. It does appear that this images issue might be related to the database and that there might be a corrupted value inside of the database which is causing this one folder to not be accessible. We have been able to add images from the 4/ folder, but could not no matter what we tried, get it to load any images in the 5/ folder.
We went as far as to create a new backup of your account and replaced all of the core files for Moodle. This will sometimes correct issues with corrupted coding inside of a script being used by the website to render its pages. This move had no effect and as such we have 2 suggestions left to assist you with this issue. Please understand that as your site is not producing any other errors than those that are visible from with-in the Administration section this does make identifying and resolving this type of issue very difficult.
Any help you can provide or any questions you'd like to ask would be much appreciated,
David