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Can the R.O. be clogged?
Yes, but not likely your problem.
Is this a whole house filtration system?
It sounds to me like its a smaller point of use unit is that correct?
Are you still there Frank?
Hold on I think I know your issue
Look at this its right out of your manual
R.O. systems take a very long time to produce water. You don' notice this when you have a storage tank that is full, however when you empty the system like you have you have to wait for it to fill the tank again.
I've installed more than my share of these and this is how they work.
Now that its had some time is it up and running?