RPi3B SD16GB balenaEtcher 2019-04-08-raspbian-stretch-full runs fine.
Either Win32DiskImager, or rpi-clone won't boot
You seems to say that BalenaEtcher is good, and WinDiskImager or Rpi-clone won't work.
Some days ago I used WinDiskImager V1.0 to create SD cards for Raspbian 2019April and everything went smoothly.
These days, to copy SD cards, I either use WinDiskImager V1.0 or the Rpi Desktop GUI accessory SD Card Copier.
WinDiskImager is good because (1) You can copy SD cards with your Win7/10 PC when you are busy with Rpi, but PC is lying idle. (2) You can use SHA256 hash to write/verify to make sure that every SD card you copy is safe and secure.
On the other hand, Rpi Desk GUI accessory SD Card Copier is good for two other reasons (1) you can copy cards freely without worrying card sizes. There is no problem copying big card to small, or vice versa, (2) You can make copies as your project progresses, say, reaching some milestones.
In those old days when the very newbie friendly Rpi CD card copier was not yet born, I did try a couple of third party clone tools. The trouble is that often they don't upgrade as fast as Raspbian OS. So every time Raspbian upgrades, I find those tools no longer work, and I need to wait update for some time, sometimes for ever, because the developer won't support any longer! (Note 1) :(
One more thing, your WinDiskImager might be outdated. For your troubleshooting, below is a record of using WinDisdImager V1.0 to install Raspbian Version 2019April and boot successfully on Rpi3B+.
A couple of years ago I tried RpiClone and found it very good, because it can copy big SD cards to small SD cards. However it is too powerful for newbies like me, who don't know about partitioning, not to mention syncing. But it is still more friendly than using other newbie scary tools like DD etc. But then Jessie upgraded to Stretch and my RpiClone no longer worked. So I had to sadly switch back from Stretch to Jessie in order to use RpiClone to copy big SD cards to small cards (I am a poor hobbyist and cannot afford to buy too many big cards. So I usually buy one or two expensive big card and many more cheapy small cards). Of course now I can use the very newbie friendly Rpi Card Copier and all bad dreams disappear and I can sleep well ever after! :)
/ to continue, ...
Win32 Disk Imager v1.0 for Win7/8.1/10 (Downloads: 57,207 This Week)
Rpi-Clone A shell script to clone a booted disk - V2.0
Balena Etcher (& Pro)