Depending on the thread brand used by the digitizer it may not translate properly to your machine format. The colors are usually close but not always exactly correct. Since yours were all dark colors it may be that they are just translated as the same color, dark gray for instance. Then it looks like the colors were combined.
Usually when this occurs the individual segments that were different colors are still there and may show up as 3 different segments all the same gray color.
A good example of this is pes format files that are digitized with Madeira colors instead of Brother colors. Purple often translates as gray so if the design already has a gray in it you get both in gray when one should actually be purple.
If your Janome allows you to change the colors when you load the design you can make changes there to help you keep up with the correct color changes. I often have to do that with my Brother ULT. I have found that I can easily get mixed up if there are several colors so I always change them in the machine so they are pretty accurate on my view screen.
You might also find out what thread brand is standard for your machine and use your Customizer software to specify that thread brand in the design before sending it to the card so they will translate correctly for you.
Just so you know this is not uncommon with so many different machines, thread brands, etc. out there. One size does not always fit all 'perfectly' every time.
Marcelle
Thank you. This is a lot of information to absorb. I just find it courious I am using Janome software (Customizer) where all colors show and print out in the template but then combine in the machine which is supposed to be set to the same thread type. I will have to do some more research with the suggestions you have given. Thanks so much. Just love all the knowledge on this site. Cuties are amazing. Becky
I have this problem, the machine seems to combine repeated colours, and they say machines can't think.
I think my machine can definite think. It waits until I step away for just a moment to break a thread or run out the bobbin. :)
I have the same program but I haven't noticed anything. Maybe copy the design again on a different stick & see what happens, Good luck!