Mrs Dotcom's evidence differed from her husband when she said she was present when the donation was discussed at a lunch.
When questioned about this inconsistency by Mr Jones, Mrs Dotcom maintained that she was there.
Mr Jones asked Mrs Dotcom if her estranged husband told her what to say. She said he did not but she did acknowledge she was still "loyal" to him.
Mrs Dotcom said she remembered "important things" from the lunch, but not "little things" like if accountant Grant McKavanagh was at the couple's Coatesville mansion that day - a point of difference between witnesses.
"I can't remember every detail of that day because it's so far away - I was there when Kim offered Mr Banks the money, I was there when he said to cut it in half."
She told Crown prosecutor Paul Dacre, QC, that when Banks and his wife visited the Dotcom mansion, Banks spoke about how hard it was to get money for political campaigns in tough economic times.
"And then Kim offered to donate $50,000 on his campaign. Mr Banks was really happy about it," she said.
"When Kim offered he asked [bodyguard Wayne Tempero] to find Grant the accountant. When Wayne got up Mr Banks spoke to Wayne, asking him to put the cheque in two [for] $25,000 so he can put it anonymously."
Mr Dotcom was surprised at the request but accepted it when Banks explained it, Mrs Dotcom said.
She said that in a later phone call between Dotcom and Banks, Dotcom asked if Banks had received the money.
"He said 'yes I did', and he thanked him."
Mr Jones suggested that conversation never happened, but Mrs Dotcom said it did.
Banks is defending a charge of filing a false electoral return in by knowingly received political donations from Dotcom and SkyCity that were recorded as anonymous.
The allegations against relate to two $25,000 donations from Megastuff Ltd on Mr Dotcom's behalf in June 2010 and $15,000 from SkyCity in May that year.
Earlier, Dotcom's lawyer Greg Towers said after his client's high-profile arrest on suspicion of copyright infringement in early 2012, he was on remand in Mt Eden Prison.
Dotcom was having problems with a thin cell mattress and asked Mr Towers to contact Banks' for help, which Mr Towers, a partner at law firm Simpson Grierson, did.
Banks told him about a conversation he had with then justice minister Judith Collins.
"He then went on to say much as he wished to publicly support Kim, that might backfire if it became known about election support etc."
Mr Towers said he didn't know what that remark was about, but later found out that Mr Dotcom had donated money to Bank's failed 2010 Auckland mayoralty bid.
In other evidence yesterday, SkyCity general counsel Peter Treacy said Banks and his rival Len Brown were each given $15,000 and SkyCity had no reason to want either contribution kept secret.
The trial, before Justice Edwin Wylie and no jury, continues.