After numerous problems, I have come to the following conclusion
Always use the Foxit PDF iFilter
Jie Li did some tests, and it is hands down the best soluition. He concludes:
"On average, FoxIT x64 PDF ifilter is still ~5 times faster than the Adobe one. But FoxIT charges 330 USD for a 2 core machine, while Adobe PDF iFilter is free. So if PDF indexing is the key to your business, go with FoxIT to get much better performance. If not, you may play with Adobe PDF iFilter to furfill some simple and basic request.