Alan,
One trick I use is to soak the brush in mineral spirits (MS) BEFORE I use it. Soaking the brush in MS, fills the bristles under ferrule with MS; it also fills the natural bristles with MS which makes them more flexible and better at laying down finish. I usually soak the brush while I'm geetting the varnish ready to brush... e.g. Shaking the varnish vigorously to ensure the flattening agent (in non-gloss) is well mixed.
I know many people say "never, never, ever shake varnish" hogwash... proper brush treatment and proper technique will eliminate the bubbles. Waterlox Sealer/Finish is already a wiping varnish so brushing it will still produce a very thin coat. Generally a brushed coat should be 2-3 wet mill thickness. I would guess this wiping varnish would be more along the 1-2 wet mill thickness.
I suspect you are getting brush strokes because you are going over it too much... Wiping varnish actualy tacks and dries quicker than the reg varnish so you can't go backover it as much.
Also the dry brush could wick some of the MS out of your finish and cause it to tack quicker. You said the most of the table (?) top is fine only some areas are showing brush strokes. What part has the brush strokes? the first part you did or the last part you brushed?
Scott
Finishing is an 'Art & a Science'. Actually, it is a process. You must understand the properties and tendencies of the finish you are using. You must know the proper steps and techniques, then you must execute them properly.