I have three tables in my app, call them tableA, tableB, and tableC. tableA has fields for tableB_id and 
The other thing is that you have your indexed columns queried as lower() , which can also be creating a partial index when the query is running.
If you will always query the column as lower() then your column should be indexed as lower(column_name) as in:
create index idx_1 on tableb(lower(foo));
Also, have you looked at the execution plan? This will answer all your questions if you can see how it is querying the tables.
Honestly, there are many factors to this. The best solution is to study up on INDEXES, specifically in Postgres so you can see how they work. It is a bit of holistic subject, you can't really answer all your problems with a minimal understanding of how they work.
For instance, Postgres has an initial "lets look at these tables and see how we should query them" before the query runs. It looks over all tables, how big each of the tables are, what indexes exist, etc. and then figures out how the query should run. THEN it executes it. Oftentimes, this is what is wrong. The engine incorrectly determines how to execute it.
A lot of the calculations of this are done off of the summarized table statistics. You can reset the summarized table statistics for any table by doing:
vacuum [table_name];
(this helps to prevent bloating from dead rows)
and then:
analyze [table_name];
I haven't always seen this work, but often times it helps.
ANyway, so best bet is to:
a) Study up on Postgres indexes (a SIMPLE write up, not something ridiculously complex) b) Study up the execution plan of the query c) Using your understanding of Postgres indexes and how the query plan is executing, you cannot help but solve the exact problem.