In 1649, a crisis occurred in Withering's official career. On the 2nd April of that year, information was laid against him "that he had assisted Lord Goring in the late insurrection in Essex (1648), by going into arms and setting out three armed men,--one with a horse,--for which he was sequestered in Essex." Shortly thereafter orders were issued for the seizure of all his money, plate, goods, rents, debts, and estate, and the Essex Commissioners were required to send up copies of all depositions against him. In May he petitioned to be freed from further trouble, alleging that he had always faithfully served Parliament. He had previously asked for the charge against him, and went down to the County Commissioners, who unanimously agreed that there was no cause for the seizure or sequestration of his estate. Thereupon orders were given "that he be discharged, and no further proceedings taken against him." About this time Witherings had a serious illness, brought on, in all probability, by the worries with which he was surrounded. He thought proper now to make his will, and in the preamble he refers to his indisposition in the following terms. He states that "he was taken upon a sudden with a dizziness in his head, and being thereupon very ill-disposed in body, yet well and perfect in memory, doth dispose, in case of mortality, his will to be," etc. Witherings was owner of the estate called "Nelmes," near Hornchurch, Essex, where was a fine old house, which still remains, and is inhabited to the present day. In 1649, one of the packet boats plying between Holyhead and Dublin, named the _Patrick_, of Waterford, was taken by the Irish; but it was afterwards retaken by Capt. Fearmes, of the _President_, and restored to its owner, the salvage due to the mariners being paid by the State. In 1650, authority was given for employing a post barque for the conveyance of letters, etc., to ply between Liverpool and Carlingford or Carrickfergus. The boat proposed was the galiot _Robert_, and the sum to be paid for its use, £11 a month. About the same time, two post barques were settled to ply between Milford Haven and the headquarters of the Lord-Lieutenant of Ireland, to carry letters "from Attorney-General Prideaux or any other public Minister." The cost of maintaining the packet boats between Holyhead and Dublin at this period was £9, 6s. 8d. each per month. In order to keep up a constant correspondence between the forces in Ulster and the standing army, a packet boat was also ordered to ply between Ulster and Carlisle.