Welcome to the forum! :icecream:
1. You have confirmed that you are a member of the guild in good standing. Your progress in the guild or University will not cause mages to stop doing business with you.
2. You might dig a little deeper into the various 'store front hours' the mages that sell or provide services have. Each can be found here by clicking on any mage in question: http://www.uesp.net/wiki/Oblivion:Mages_Guild#Members
3. If what you mention cannot be explained away by 1 or 2 above, then it is a glitch. Since it would be a glitch that is not well-known, that means it would likely be caused by various mods interfering with each other.
If you can rule out 1 and 3, then I would refocus very carefully on number 2.
Good luck.