You could be experiencing one or more issues that are preventing the air from being purged from both drains.
I have to assume that you have VGB compliant drains. If that is the case, the suction line could have been plumbed
1) in series (or) straight in line with the drains
2)the drains are of unequal height
3)one drain is closer than the other if plumbed with a center tee
4)you don't have enough air volume
Any combination of the above could create a situation where air bubbles won't escape equally.
I would suggest that you either turn the pump on and dye test both drains to prove they're working or increase the volume of your air source.
Many times a vgb drain will suck great but not purge very well.
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