Did you by any chance start using a different printer to print your labels?
The "print area" of different printer models varies and this difference can affect how your labels layout prints.
Label layouts consist of three parts usually: Header, Body and Footer
You'll find matching parts to your page of layouts.
IF the header is two large or a top margin has been specified, the labels could print lower down on the page.
This could also leave the last row of labels blank like you describe when FileMaker.
To fix this:
Enter layout mode.
Select your printer and the correct page size and orientation for printing labels.
Go to Layout setup... and see if "use fixed page margins is enabled. If so, note the size of your top and bottom margins.
Return to the layout check the size of each layout part by clicking the part label and then checking the size in the height box found on the inspector's position tab. (You can change the units used in these boxes by clicking them until you get the units you want.)
The height of the top margin + the height of the header should equal the height of the header strip on your labels page. The height of the body should equal the distance from the top edge of one label to the top edge of the next label below it. The height of the footer + the height of any bottom margin should = the height of the bottom strip on your labels page.
You may need to change the Inspector's position/size boxes to pixels and make very small adjustments to these part sizes until the labels print correctly.