Your problem is most likely due to the crossing construction itself since there are fairly long non-conductive sections (i.e., plastic) your loco passes over resulting in it getting electrically ‘stranded’. They are made this way so that you don’t create a short circuit when passing over the other cross track. There isn’t really much you can do aside from buying locos that have longer electrical pick up points across the engine’s length which will bridge the power gap. Some manufacturer’s use more of the wheel base area to prevent this problem but if you are using a shortie loco switcher like a 44 tonner or an 0-4-0, I think you are stuck.
One option that MAY work is to replace the crossing with a different manufacturer (like Peco) that may have shorter unpowered sections or gaps.

Hope this helped –

Geof from the US