Largely inconsistent query execution speed, involving psql_tmp

While executing the following query through psql :

SELECT me.* FROM measurement_events me JOIN msrcs_timestamps mt ON
me.measurement_source_id=mt.measurement_source_id WHERE measurement_time >
last_update_time

there are two behaviors observed by postgresql (8.4):
1) Either the query performs lots of reads on the database and completes in
about 4 hours (that is the normal-expected behavior)
2) Either the query starts filling-up pgsql_tmp and this causes large write
I/O on the server, and the query never actually completes on a reasonable
time (we stop it after 10h).

For some strange reason, behaviour 2 is always observed when running psql
through a bash script, while behavior 1 is only observed while running psql
interactively from command line (but not always).

explain:
# explain SELECT me.* FROM measurement_events me JOIN msrcs_timestamps mt
ON me.measurement_source_id=mt.measurement_source_id WHERE
measurement_time > last_update_time;
QUERY PLAN

----------------------------------------------------------------------------------------------
Hash Join (cost=10111.78..422893652.69 rows=2958929695 width=103)
Hash Cond: (me.measurement_source_id = mt.measurement_source_id)
Join Filter: (me.measurement_time > mt.last_update_time)
-> Seq Scan on measurement_events me (cost=0.00..234251772.85
rows=8876789085 width=103)
-> Hash (cost=5733.57..5733.57 rows=350257 width=24)
-> Seq Scan on msrcs_timestamps mt (cost=0.00..5733.57
rows=350257 width=24)
(6 rows)

We have tried so far fiddling with work_mem up to 512M - no difference.
Any suggestions?

Thanks for any help,
-Spiros Ioannou
inaccess