Answer:
It may be difficult to make a case that anyone's Fourth Amendment rights were violated in Marbury v. Madison.
Amendment IV
"The right of the people to be secure in their persons, houses, papers, and effects, against unreasonable searches and seizures, shall not be violated, and no warrants shall issue, but upon probable cause, supported by oath or affirmation, and particularly describing the place to be searched, and the persons or things to be seized."
Maybe one could argue Marbury's commission was illegally seized or that withholding the paperwork prevented him from being secure in his "...papers, and effects..." but it would be difficult to apply this concept to something that was never in Marbury's possession. The Fourth Amendment applies when there is both a "search" and a "seizure," and pertains primarily to privacy rights. Marbury was never subject to an invasion of his person or belongings, with or without a warrant.
Marshall held Marbury was entitled to receive his commission, but the deprivation was a civil matter, not criminal.
Likewise, the Fourth Amendment has no application to the commissions relative to the government officials, Adams, Marshall, Jefferson, or Madison (actually Levi Lincoln), because the paperwork and premises belonged to the government, not to any of them, personally.
Case Citation:
Marbury v. Madison, 5 US 137 (1803)