What makes you say so? At first I thought your issue was on ElectrumX and I would have mistyped them considering it as a software. But now you are saying so, you are using software and not server. If your issue is negative confirmations and it is in electrum software/merchant wallet then what I have said is right.

So you are mentioning about this right? : http://docs.electrum.org/en/latest/merchant.html