I have experienced the same issue and found a fix and/or bug in how Intellij auto populates the path for the manifest.
INTELLIJ UI
When creating an artifact to create jar files, IntelliJ auto populates the the path where the current manifest is located.
i.e. After choosing Main-Class in the artifact creation page, Intellij will add automatically the following path srcjavaMETA-INFMANIFEST.MF. For some reason, the build command never takes the mentioned MANIFEST.MF File. It creates one from scratch without the Main-Class definition which results on the "Failed to load Main-Class"
If using the IntelliJ UI to create jar artifacts; removed the auto populate path by changing it to /$PROJECT_DIR/src/
and click OK.
Example of what it looks like by default:
Now this is what it should look like after the change:
MANUAL FIX TO ENTER CORRECT MANIFEST.MF FILE
On the IntelliJ project , open .ideaartifacts\_jar.xml
Make sure it contains
<element id="directory" name="META-INF">
<element id="file-copy" path="$PROJECT_DIR$/src/META-INF/MANIFEST.MF" />
</element>
You might need to reload intelliJ once you do this so it picks up on the changes to the .xml file
For me it happened on maven projects where a different structure exists (i.e. src/main/java/..).
I am using OSX 10.9.2 with IntelliJ version 12.1.6
Hope that helps.
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