Event not displayed in Kibana, displayed in stdout

[zuokuok]

I have seen this (only) thread about the same issue as me, but doesn't work for me.

Logs that are visible in stdout not showing up in es/kibana

My output plugin is using BOTH stdout { codec => rubydebug } and an elasticsearch output connecting to our cluster, I do this sometimes to help me debug. When I run a test script to send a bunch of data to logstash, with stdout enabled, I am having the incredibly strange experience where I see all of the data in my stdout screen, looking directly into logstash, and yet only about half of the data shows up in the corresponding index in kibana. Neither logstash nor elasticsearch produces any lo…

Could someone say what are the things to watch out for in the data?
In which file should I look to find what was rejected? Are there information (kind of like a stacktrace)?

To give an example of what the structure of the message looks like:

This is not displayed in Kibana (but it is in stdout):

[10/13/17 9:02:44:919 CEST] 000000be ht.integration.js.JavaScriptIntegrationLibraryImplementation I {"operation":"some json data","CreationDateTime":"2017-10-13T09:02:44.653+02:00" ... (rest of valid json payload)

This is displayed in Kibana:

[10/13/17 13:42:49:720 CEST] 00000171 ht.integration.js.JavaScriptIntegrationLibraryImplementation I {"operation":"some json data","CreationDateTime":"2017-10-13T11:42:44.480"" ... (rest of valid json payload)

Note that I kept the CreationDateTime in the example as a potential problem with the +02:00, but I actually remove it from the string before sending it to ES.

Also very important: when I remove all filters, the event is actually displayed on Kibana.
What I don't understand however is that my filters are valid, and the expected output is given in stdout.

I also debugged with the grok debugger, patterns are fine.