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Was she trying to avoid questioning about the Holy Land matter? Is this the same grand jury panel that was investigating that leak? If not, could he even ask her about it? Can a grand jury "combine" two investigations during the testimony of one witness?

I think the answer to those amounts to "no," regarding Miller and the Holy Land matter. More below on that.

The more plausible reason is that she had another source she's still hiding. Libby has already testified about his discussions with Miller.

That makes sense too, and I am drawing a blank on the charge to the investigator. If the charge is to uncover government leaks (which is what I think it was), then Fitzgerald may be happy to avoid questions outside of that - other than probing obstruction of getting to the bottom of "government leaks." Fitzgerald wants to get to the bottom of the case he's chartered with, and needs Miller's testimony. He is willing to play hardball to get it. She'd had enough at 85 days, and didn't want the time or other baggage that comes with criminal contempt. Maybe she was willing to be used as a pawn to advance a federal reporters shield law. Her name and situation was used liberally in testimony before Congress.

OK, here is what I've stumbled across regarding Miller and the Holy Land Foundation matter.

U.S. Attorney Can't Force N.Y. Times to Supply Documents
By John Mintz - Washington Post Staff Writer
Friday, February 25, 2005; Page A03
U.S. District Judge Robert W. Sweet ruled that a federal prosecutor in Chicago cannot compel the newspaper to turn over records of two Times reporters' phone calls in 2001 as part of an investigation into possible government leaks. The effort by U.S. Attorney Patrick J. Fitzgerald came in the cases of two Muslim charities accused of possible ties to terrorists. ...

Link to Sweet's opinion -> http://www.fas.org/sgp/jud/nyt022405.pdf

On Dec. 3, 2001, Times reporter Judith Miller telephoned officials with the Holy Land Foundation for Relief and Development, a Texas-based charity accused of being a front for Palestinian terrorists, and asked for a comment about what she said was the government's probable crackdown on the group.
U.S. officials said this conversation and Miller's article on the subject in the Times on Dec. 4 increased the likelihood that the foundation destroyed or hid records before a hastily organized raid by agents that day.
On Dec. 13, Times reporter Philip Shenon called the Illinois-based Global Relief Foundation and asked for comment about the government's intention to freeze its assets because of allegations it had ties to terrorists. "FBI personnel learned that some of the targets [of the investigation] may be destroying documents," and agents "hastily assembled" a raid on the charity on Dec. 14, according to a report by the commission that investigated the Sept. 11, 2001, attacks.
http://www.washingtonpost.com/wp-dyn/articles/A51840-2005Feb24.html
New York Times Co. v. Gonzales, 04 Civ. 7677 - (Case involving telephone records of reporters Judith Miller and Philip Shenon.) "Based upon the Second Circuit's interpretation of Branzburg in the cases just described, district courts in this circuit have recognized the existence of a qualified reporter's privilege derived from the First Amendment. In view of the foregoing, it is concluded that the Second Circuit, based on Branzburg, has recognized a qualified First Amendment privilege, applicable in civil actions and in all phases of a criminal prosecution, that protects reporters from compelled disclosure of confidential sources. Pursuant to this qualified privilege, the party seeking disclosure must make `a clear and specific showing that the sought information is: [1] highly material and relevant, [2] necessary or critical to the maintenance of the claim, and [3] not obtainable from other available sources.'"
http://www.firstamendmentcenter.org/analysis.aspx?id=15525
The Reporters Committee for the Freedom of the Press reports that an appeal was filed in late May 2005.
http://www.firstamendmentcenter.org/about.aspx?id=15634

New York Times v. Gonzales, 04 Civ. 7677 is cited often, but I haven't found its track in the appellate courts. The NYT v. Gonzales case is -NOT- part of the legal action relating to Fitzgerald's investigation into the Plame Leak. That legal action involved a February 15, 2005 decision by the D.C. Circuit Court. The petition for rehearing en banc was denied, and certiori was denied by the Supreme Court.

At any rate, Fitzgerald is presently bound by the lower court's decision in NYT v. Gonzales, and therefore cannot compel testimony regarding the telephone records, etc. of the Holy Land Foundation. That case is still working its way through the courts, and any links to current status of the case will be much appreciated.