Thoughts on using dark stain vs replacing boards for a messy install?

I had a similar issue with my Western Red Cedar deck two years ago. The crew used a chalk line initially but then got lazy toward the stairs. If the screws are zig-zagging more than a half-inch, it’s going to bug you every time you sweep. Cedar is soft, so those holes really stand out once the wood starts to weather and shrink slightly. Regarding the dark walnut stain, in my experience, it actually highlights the imperfections rather than hiding them. If you use something like Penofin or Messmer’s, the oil tends to pool slightly around the screw heads and makes the irregular pattern even more obvious. A dark color creates a sharp contrast against the metal of the screw unless you specifically used color-matched heads, which many crews skip. I’d definitely ask them to come back and fix the worst sections. If they’re the type to work thru a heatwave, they probably have some pride in the job and just hit a wall. Swapping out a few 5/4 boards now is much easier than trying to live with it or hiding it under a rug. You paid a premium for cedar beacuse it's a beautiful material; don't let a sloppy afternoon ruin the long-term look.

Honestly, once you get your grill, some planters, and a high-quality outdoor rug down, you won't even notice those screws. I went thru the same anxiety with my own project back in 2019. I was measuring every gap and obsessed over the joist alignment. Fast forward six months, and between the natural weathering and the general wear and tear of hosting, the "perfect" lines I wanted didn't matter one bit.

Cedar is a character wood. If you go with a heavy-bodied stain like Cabot’s Cordovan Brown or even a semi-transparent dark walnut, the pigment settles around the screw heads and acutally helps them recede into the grain. Swapping boards now just risks splitting the cedar or leaving visible scars on the pressure-treated frame underneath. Give it a season. Once the wood moves a bit and you’ve got a patio set from Costco or West Elm out there, the minor zig-zags will be the last thing on your mind.

If they didn't use a Camo Marksman Pro or at least snap a line for some #10 2.5-inch GRK Pheinox 305 stainless screws, they were rushing. Heatwave or not, sloppy lines usally mean they’re missing the center of your joists, wich is a recipe for split ends once that cedar hits 12% moisture content.

Check if they used 304 or 305 stainless. If they used standard coated screws, the tannin bleed will make those "messy" holes look like black ink splotches in six months. I'd demand they sister the joists where they missed and re-run the boards. At $4+ a linear foot for clear cedar, "sloppy" shouldn't be in the vocabulary.

If you decide to pull those boards, just grab a Kreg Deck Jig. It moves the fasteners to the side so you don't have any visible holes on the face to obsess over. It’s way better for cedar since it prevents those surface splits that eventually happen. If you're keeping the layout as-is, swap the messy ones for Simpson Strong-Tie Trim-Head screws in black. The heads are tiny and basially vanish into the grain compared to those chunky standard screws.

I dealt with a messy screw line on my front porch and realized the crew missed the joists entirely on the crooked ones. I didn't bother with fancy jigs; I just cut a 6-inch block of scrap wood, drilled two pilot holes exactly where I wanted them, and used that as a guide for the replacement boards. It kept my lines dead straight without me having to overthink it.

One thing to check—run your hand over those boards. If the screws aren't sunk perfectly flush, you're going to catch your toes on them for years. Better to reset them now while the cedar is still soft and fresh.

I'm still learning the basics here, but if you pull those boards up and redo them, what happens to the joists underneath? I'd be scared that putting more holes in the support frame would make it weaker or let water in. Is there a way to 'plug' those old holes so the wood doesn't rot? Sorry if that's a dumb question, I'm just trying to figure out if re-doing it causes more hidden problems.