The holes in the pop-up assembly are to allow water to flow down the overflow hole in the sink and fall into the drain pipe... supposed to be like that...
In terms of that leak you're talking about, take the pop-up assembly apart and then reputty the top part like you did last time, and this time spin the nut and washer (RP6140
) and push the rubber gasket (RP6142
) down tight away from the sink. Add some pipe dope
(pipe thread sealant... see image) to these threads and then install the assembly by spinning the nut as you normally would... this will pull the gasket up and into place. This can be a little annoying in that it makes the job take longer (spinning nut and gasket up to the sink), but the pipe dope on the threads with the gasket should finish sealing this up permanently!
The putty will seal the top part (RP23060
Did you have threads on 1.25" tailpiece (RP6128
) on the bottom 1/2 of the assembly? If so, these threads need to have pipe dope applied as well.
Let us know if this made sense.. OK?