Labeled image instance export doesn't work as expected for z-stacks

[petebankhead]

Bug report

Describe the bug
Exporting annotations across multiple z-slices can fail, in that annotations are drawn on more slices than they should.

To Reproduce
Steps to reproduce the behavior:

1. Create a QuPath project containing the ImageJ sample image 'Confocal Series' (accessed via File → Open Samples
2. Import the attached .geojson file (rename .txt to .geojson) - can import via drag & drop
   • confocal-series-small.txt
3. Attempt export using the script below:

double downsample = 1.0

def imageData = getCurrentImageData()

def labelServer = new LabeledImageServer.Builder(imageData)
    .downsample(downsample)    // Choose server resolution; this should match the resolution at which tiles are exported
    .useInstanceLabels()
    .useAnnotations()
    .multichannelOutput(false) // If true, each label refers to the channel of a multichannel binary image (required for multiclass probability)
    .build()

def path = buildFilePath(PROJECT_BASE_DIR, "labels.tif")
writeImage(labelServer, path)

Expected behavior
A TIFF stack is written that contains 3 annotations on different z-slices.

Screenshots
All 3 annotations are included on slices where only one should appear.

Desktop (please complete the following information):

• OS: macOS (probably all)
• QuPath Version: 0.4.3

Additional context
Problem first noticed when replying to https://forum.image.sc/t/exporting-annotations-for-all-z-stack/81393/3

[petebankhead]

The bug only seems to surface for instance labels and indexed image output.