Migration from solr 3.6.1 to 4.4 - custom analyzer

Migration from solr 3.6.1 to 4.4 - custom analyzer

I have problem with migration from solr 3.6.1 to 4.4.
In schema I have fieldType with custom analyzer, and field "content" that
use this type.
In data-config I have 2 main entity sections:
1) fetch data from wiki
2) fetch data from binary files by Tika
On 3.6.1 everything worked fine.
On 4.4 after executing data import, I am getting status which inform that
all documents that I want has been processed.
After executing this query "*:*", I am getting all documents that I want.
But when I trying to search by specific words from "content" (e.g.
"content:project") I've get only documents from wiki.
I check my indexes, and it seems that I have only terms from wiki.
When I change order in data-config:
1) fetch data from binary files by Tika
2) fetch data from wiki
I have only terms from binary files.
Second problem is that altough I have some data indexed sometimes the same
query return results, sometimes not.
Without my custom analyzer everything works correctly (when I use type
text_general from example),
it should point that problem lies in my custom code,
but when I use analysis from admin panel on "content" field everything
looks good.