It does matter because there is ferts and fert salts sitting in the medium and it's in constant contact with your roots....mine way outgrow the buckets also but I still get the problem. Use RO or distilled water to rinse through them....check the runoff of what you get out of each basket.....both ppms and ph. Rinse them through several times....ro or distilled ph correct water only. That's how I do them usually excetp at the end of the grow. The buildup is most likely strictly in your medium.