> This year, i'm grafting by hand, using a size 00 pen, which i found even
easier than using the > Jenter thing.

Have you tried the Chinese grafting tools?

> After the cells are capped, i put protectors on them.

Why are you using cell protectors?  Unless conditions are very bad, the
finishing colony should not pull them down.

> The cell will contain one of three things:
> -A small undeveloped bee, maybe a worker bee, still white with purple eyes

If the larvae are still white then they have a day or so to go to hatch.  If
it is the day they are due to hatch they should be starting to turn brown.

> -A small fully developed, but dead, bee

Are they getting chilled because of the cell protectors?

> -A black mess on the bottom of the cell (rare)

Have you had the "mess" checked for black queen cell virus?  Your
description seems to fit BQCV.  Also have it checked for European foulbrood.
EFB can kill queen larvae.

Have you ever tried the "Cloake" method of queen rearing?  It was developed
by Harry Cloake from New Zealand and uses the one colony for starting and
finishing.  I use a slight variation on it.

Trevor Weatherhead
AUSTRALIA

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