I have the Babylock Ellisimo which is the sister machine to your Brother 6000D...and I use prewould Class 15A bobbins from Metro Embroidery with absolutely no problems...I don't think that your size would be the Class M...if anything it would be Class L bobbins...I think the little metal insert for your bobbin case is to make the Class L bobbins raise up a bit to be the same height as the Class 15A bobbins. Not sure who you are getting your prewound bobbins from...perhaps they are not exactly to spec? Not sure, but I think your machine does use Class 15A...If your manual shows 7/l6", measure the bobbins you have and see how they compare...I know that the Class L bobbins are a tad bit thinner than the Class 15A..I have included the link to Metro Thread so you can take a look at the differences in the bobbins sizes...

I use the Janome prewound bobbins in my Quattro and have no issues at all.

The little top had is used with the shorter bobbins (many of the prewounds are the shorter ones). So if the prewounds you are using are shorter than the bobbins that came with the machine you need the top had to make them feed correctly. I use the short metro prewounds all the time with the top hat and have no problems.

I pretty sure your machine uses the Class A size 15 bobbins as they are 7/16" size.

Your little metal top hat is used if you have L sized pre wound bobbins which are only 5/16" tall and are not as tall as the size A pre wound bobbins. So you have to set the L sized bobbins on the little metal top hat to raise them up so they will work in the bobbin case right.

I think the M sized pre wounds are for certain Industrial machines/ Commercial machine. They are as tall as the A sized pre wound bobbins but are much wider around (1") and would need a larger bobbin case to fit into.

See the chart below at the link.

What problems are you having with the A sized pre wounds.
Are you sure you have them in the bobbin case the right way?