The 23-year-old, who missed much of last season with a knee problem, is currently in Merseyside to finalise an £8.6m move to Goodison Park.
Twente chairman Joop Munsterman revealed on Tuesday evening that talks had reopened because the Blues have tried to "renegotiate" the deal to protect them financially, should the injury reoccur.
He is quoted in the Daily Mail as saying: "Everton have demanded additional conditions for the transfer of Leroy. They want to pay in separate instalments. We can't agree with that."
The fee for Fer is believed to be staggered due to performance-related bonuses.