Ok, like Lukáš Fryč said it's clear was is going wrong ( notice servedVariants < totalVariants ) but :

• I'm not able to reproduce it anymore
• I don't know what could wrong here but a lack of knowledge here around the jms stuff.

Some pointers, for those who want to look with me

Looks like, when it goes wrong, this is never hit : https://github.com/aerogear/aerogear-unifiedpush-server/blob/master/push/sender/src/main/java/org/jboss/aerogear/unifiedpush/message/MetricsCollector.java#L98 , probably because the condition notice{{areAllBatchesLoaded}} before is not met.
This condition uses https://github.com/aerogear/aerogear-unifiedpush-server/blob/master/push/sender/src/main/java/org/jboss/aerogear/unifiedpush/message/jms/AbstractJMSMessageConsumer.java#L54 so something could go wrong there.