I have now learned to use LRTimelapse for a month, but I don't understand why the WB setting is really off after I have saved the metadata and reading it again in LR.

Every time WB is set really red after the saving, but it doesn't show that way anywhere in LRTimelapse. I know it's easy to fix in LR, but still..

Camera is D90 and WB setting is auto.

The explanation is the following: When initializing Metadata, LRTimelapse does not know anything about the White Balance. So it just sets a default value for initialization. Normally you would like to manually edit the WB for the keyframes anyway so this doesn't matter.
If you instist to use the value set in the camera, you can set it back to "As Shot" and start from there. You only have to do this for the first key frame since you are going to copy and modify this value to the next ones.