Performance difference between SQLITE 3.7.13 and 3.8.0

Question

Changing SQLITE version has huge performance impact for our queries. We have observed a speedup of over 25 on some queries, although at the same time we observe a slow down of up to 2 on others. What could be causing this performance difference?

When comparing execution times, only the execution environment changes. Same hardware, same DB, same query. SQLITE is being used through Perl DBI.

Run time of query 1:

 SQLITE 3.8.0(Fedora 19):
 real   0m0.674s
 user   0m0.650s
 sys    0m0.021s

 SQLITE 3.7.13(Debian Wheezy):
 real   0m17.242s
 user   0m17.169s
 sys    0m0.028s

Run time of query 2:

 SQLITE 3.8.0(Fedora 19):
 real   0m0.303s
 user   0m0.284s
 sys    0m0.017s


 SQLITE 3.7.13(Debian Wheezy):
 real   0m0.168s
 user   0m0.160s
 sys    0m0.007s

Not sure if it is useful, but some parameters used to tune the DB:

 PRAGMA synchronous = OFF
 PRAGMA journal_mode = OFF
 PRAGMA locking_mode = EXCLUSIVE
 PRAGMA temp_store = MEMORY
 PRAGMA PAGE_SIZE = 4096
 PRAGMA cache_size = 125000

Answer 1

Thanks to the help of @CL., I went to the next generation query planner page that mentioned low-quality index as being "one where there are more than 10 or 20 rows in the table that have the same value". I had one index for a table containing only repeated foreign keys. Dropping the index fixed the issue.