Cannot access all my folders from my SDCard via USB
You could try installing the Rescan SD Card! app and running it. You don't mention what phone you have sometimes you need to tell Android to scan the sd card to pick up changes.

This answer over at StackOverflow appears to suggest that sometimes the MTP cache gets out of date until a reboot of the phone or an app such as Rescan SD Card! is used. This no longer works as of Android 5.0.2, and a reboot of the device is the only fix.