Quick test to see if ground glass = film plane:
Set up a ruler/yardstick at an oblique angle to your camera. Use a longish lens up close, wide open. Focus on a particular mark (e.g., the 6" mark) and make an exposure. Do not stop down. Develop the film and see if the focus is shifted from the focus on the ground glass. If so, the film plane is likely different from the ground glass. You'll need to remedy this by 1) checking the placement of your Fresnel to make sure it is correct and 2) shimming or otherwise repositioning the ground glass so it is in the proper position.
Other causes of out-of-focus:
Your lens has an issue. It could be as simple as an element not screwed in all the way or having lost a spacing shim during disassembly or something as catastrophic as having dropped the lens and misaligned an element. Make sure this happens over several lenses. If not, look to the lens in question. I had a 300mm lens that wouldn't focus correctly till I discovered that the rear element was not seating properly due to interference with an overly-thick lens board. Do check for cloudiness, scratches, etc. if one lens is the culprit.
Camera shake. Camera movement has a specific look under magnification, so examine your negatives under magnification (in the enlarger with a grain focuser is good). Look for directional blur, double images, etc.
Film holder seating problems. Make sure your film holders are seating properly and that there is not debris or other obstacles holding the film holder away from its engineered position. Something like a doubled-over light baffle or gunk can make a big difference.
Film loading problems. Check your negatives to make sure the rebates are all there and squarely-aligned with the film edges. If not, you may be loading your film with one edge outside the guide channel.
Ground glass seated improperly. If you've had the ground glass off your camera for cleaning or whatever, it may have gone back together not properly aligned. You may have lost a shim or got something blocking proper seating of the focusing screen. Check to make sure everything is as it should be.
Another suggestion. Try not focusing stopped down to taking aperture. Your focus will be more accurate if you focus wide open as long as your lens does not exhibit focus shift. The bandwidth of acceptable focus increases as you stop down (hence DoF), but that can keep us from easily identifying the sharpest point of focus.
Also, make sure that locking down your focus is not introducing some movement. Likewise, make sure that inserting the film holder is not shifting the back, etc., etc.
If your problem is happening only occasionally, i.e., "every second time," then look for one of the causes that is consistent with that scenario, such as particular lens, moving something when locking down or inserting the holder, etc.
Hope you find your problem,
Doremus
