All known bugs are fixed in the V2014.09 release today and an email notification will go out soon.

You need to download the official release as even more bugs were fixed.

http://www.pcblibraries.com/forum/library-expert-201407-released_topic1393.html 

I do have one comment to make so that when we do release V2014.07 you'll know what to expect for the Micro-miniature Chip component family.

The new Courtyard Excess values that you are changing (like 0.10 mm for the 01005 package) will be affected if you have silkscreen outlines. There is a rule that all silkscreen outlines must be inside the courtyard and thus the program will automatically push the courtyard out if it needs to meet this rule.

The silkscreen outline has a higher priority than the courtyard.

Hopefully, once all code is validated and approved V2014.07 will be released tonight.

Are you using "User" or "Default" preferences? User creates a 1-Tier library system. Default creates a 3-Tier library system, but you need to create a custom Default Preference file for that.

If you are using "User" preferences then in the "Setup > Design > Surface Mount Environment" must be set to "User". If this is not the case then we need to take this off-line and do a webcast after you install V2014.07 which will be released soon (today).

Very nice! I like those settings.

In running my tests, Whenever I change the User Preferences and save (Done), the program auto-resets the values back to the original only for the < 1.0 mm and < 0.5 mm

The < 1.6 mm and >= 1.6 mm are working OK.

We get this issue fixed ASAP and release V2014.07 today.

First, I hope you are using the V2014.06 release because I cannot reproduce your issue with that version.

In User Preferences there are now 4 different versions to allow you more flexibility for smaller and smaller Chip components. You need to make sure that you adjust all of them.