Extra-long wait in merge phase

When running INSERT INTO <table> <select statement> in 10 min intervals to aggregate data from temporary tables and insert it to main datastore. All goes perfectly, but after 4-5 hours we observe that insert runs 10-100x times slower. In iqmsg logs we see following:

for 'long' insert:

I. 05/20 07:50:05. 0000021624 Load phase completed

I. 05/20 07:50:05. 0000021624 Merge in progress: 45%

I. 05/20 07:50:05. 0000021624 Merge in progress: 67%

I. 05/20 07:50:05. 0000021624 Merge in progress: 90%

I. 05/20 08:46:11. 0000021624 Merge in progress: 100%

I. 05/20 08:46:11. 0000021624 Merge phase completed

I. 05/20 08:46:11. 0000021624 [20896]: Insert for 'natflow_20_05_2016' completed in 3422 seconds. 9024346 rows inserted.

for 'normal' insert:

I. 05/20 09:10:16. 0000000133 Load phase completed

I. 05/20 09:10:16. 0000000133 Merge in progress: 45%

I. 05/20 09:10:16. 0000000133 Merge in progress: 67%

I. 05/20 09:10:16. 0000000133 Merge in progress: 90%

I. 05/20 09:10:25. 0000000133 Merge in progress: 100%

I. 05/20 09:10:25. 0000000133 Merge phase completed

I. 05/20 09:10:25. 0000000133 [20896]: Insert for 'natflow_20_05_2016' completed in 23 seconds.  18966510 rows inserted.

no other activity in database, only inserts. After restarting SAP IQ all goes to normal until next 5 hours.