While at court he accused Sir Henry Lee of Ditchley of treason, with the "most indecent and contumelious words", and Lee's cousin, Thomas Lee (a captain in the Irish service who was later hanged for his involvement with the coup attempt of the Earl of Essex), wrote to Cecil seeking the opportunity to meet the charges.
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He complained that Cashel was only worth £98 and – in spite of the misgivings of William Cecil, Lord Burghley – was granted the See of Waterford and Lismore in commendam, which he held until 1589, and then again from 1592 upon the death of Bishop Wetherhead.
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The estate of Lismore had been sold by him to Sir Walter Raleigh for a nominal price, although he kept the capitular seal of Cashel.