Detectives investigating the disappearance of Lynda Spence, 27, in April 2011 noticed different floorboards during a search of a flat in West Kilbride, Ayrshire.
Accused David Parker, 38, told police during question-ing the loft conversion space in his home was used to hold Ms Spence in exchange for a promised £1500.
He and three others deny torturing the business-woman to extract financial details, murdering her and cleaning the flat to hide evidence.
Detective Constable James McAteer, 38, who examined the flat in Meadowfoot Road, told the trial at the High Court in Glasgow that he noticed "a few different floorboards".
Looking at a number of lettered floorboards shown in a photograph to the court, he said: "I felt that A, B and C had not been fitted by a tradesman but D had been."
Owner of the flat James Dillon, 42, who rented it to Parker for several years, identified "two new pieces of flooring that I never fitted" when shown a photograph of a section of the floor.
"A, B and C are new pieces of flooring," he said.
Mr Dillon has since sold the flat.
Parker is accused along with Colin Coats, 42, Philip Wade, 42, and Paul Smith, 47.
Jurors were last week shown video footage of the loft space and police pictures of two blood spots in the bathroom area.
It is alleged that during the fortnight she was held hostage, Ms Spence was burned with cigarettes and an iron, was struck on the legs with a golf club and had her thumb cut off.
The court has heard evidence that prior to her disappearance she was involved in a business deal in which Coats had a stake.
Prosecutors claim that after she was murdered the men used bleach to clean the flat, removed carpets and floorboards and set fire to some of the property's contents.
Joiner Mr Dillon said he had renovated the bathroom in October or November 2010 after a leaking pipe caused damage.
He carried out further work following a burst pipe at the property a few months later.
Derek Ogg, QC, defending Coats, suggested water damage would have made the carpets "smelly".
Mr Dillon said he had thoroughly cleaned the flat when he had carried out the work.
Mr Ogg asked the witness: "Both events would have given rise to rubble and rubbish in the back garden?"
Mr Dillon agreed.
The trial continues.