Further to my post, John and Margaret Mallery were not originally from Kenilworth as their family only appear in the parish registers there from 1676. So I have been trying to see where they were before.
I found a reference to a John Mallery of Hatton in the early 1660s and also in Hatton was a John Rutter.
I then had a look at the Hatton marriage register transcribed here
https://archive.org/details/warwickshirepari03phil in which a John Rutter married Martha Rawbone in 1624.
At the Warwickshire County Record Office (ref CR 611/204/1-13) is a document which states that John Rutter of Hatton became at trustee in 1652 of the Throckmorton's Charity.
The 1677 marriage agreement of John and Margaret Mallery's daughter Mary Mallery to Joseph Mason include the name of John Bree of Beausale, gentleman.
While the registers of Hatton are somewhat defective from the 1640s to early 1700s, there are some baptisms of a John Bree in Hatton in the 1650s. Beausale was in Hatton.
John Mallery and John Bree's grandchildren John Mallery (1687-1732) and Elizabeth Bree/Mallery/Brockhurst (1690-1735) married in Warwick in 1721 and resided in Leek Wootton.
Taking all the above into consideration it seemed probable that my ancestor Margaret Rutter/Mallery was the daughter of John Rutter and Martha Rawbone who married in 1624.
Now the later registers of Hatton from the 1640s/50s to the early 1700s are somewhat defective, but on freereg I then found the baptism of Margaret Rutter, daughter of John Rutter, in Hatton in 1625.
This all seems to prove who Margaret Rutter/Mallery (1625-1686) was and that her mother Martha Rutter was born Martha Rawbone at some point prior to c1608 and died after 1686.
I assume from John Rutter being a trustee of the Throckmorton Charity in 1652 that connections here somehow led to this payment being due to Clement Throckmorton.
Thanks again for the replies.
Jon