To remedy that you can capture long floats by adding a simple twist at the midway point, keeping to the orientation you have established in your yarn management (new under old, for example). This way instead of one long float you have created two shorter ones. These captured floats also block nicely because there is a little bit of possible movement if your twist your yarns correctly.
This video on Stranded Colorwork Technique can tell you a lot more about knitting intarsia, by working on a stranded beanie hat.
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