The Los Angeles Times article cited in my post below notes the following problems with the redistricting initiative: “according to backers of the initiative, it gives legislative leaders one day more than the Lockyer-approved version to select the retired judges who would draw the districts. In addition, the preamble of the initiative is condensed from five paragraphs to four in versions displayed by signature-gatherers on the street.”
The question whether the initiative should be disqualified from appearing on the ballot appears to turn on whether the petitions were in “substantial compliance” with California law. Although backers of the initiative claim that it is, I am not so sure.
Here is a useful statement of the substantial compliance doctrine, from Ruiz v. Sylva, 102 Cal.App.4th 199 (2002):

The failure to provide information or the communication of misinformation–threaten the proper operation and the integrity of the election process. (San Francisco Forty-Niners v. Nishioka (1999) 75 Cal.App.4th 637, 642, 89 al.Rptr.2d 388.) No court has applied the doctrine of substantial compliance to save a petition that provides confusing or misleading information. (Clark v. Jordan, supra, 7 Cal.2d 248, 60 P.2d 457 [finding no substantial compliance where short title does not reveal initiative measure would affect taxes]; Mervyn’s v. Reyes (1998) 69 Cal.App.4th 93, 104, 81 Cal.Rptr.2d 148 [omitting 17 pages of general plan section did not constitute substantial compliance]; Hebard v. Bybee (1998) 65 Cal.App.4th 1331, 77 Cal.Rptr.2d 352 [no substantial compliance where title of ordinance in referendum petition was inaccurate]; Ibarra v. City of Carson (1989) 214 Cal.App.3d 90, 99, 262 Cal.Rptr. 485[“[w]here the purpose of the statutory requirement is to give information to the public to assist the voters in deciding whether to sign or oppose the petition, the substantial compliance argument is often rejected and strict compliance held essential”]; Creighton v. Reviczky, supra, 171 Cal.App.3d 1225, 1231, 1338, 217 Cal.Rptr. 834 [finding no substantial compliance where proponents increased confusion by excluding test of protested legislation].)
In contrast, the doctrine of substantial compliance has been applied where only the emphasis of the information presented is at issue. For example, in California Teachers Assn. v. Collins (1934) 1 Cal.2d 202, 34 P.2d 134, the registrar of voters refused to accept a petition because, in part, the short title was printed in 12 point instead of 18 point type, when section 1197b of the Political Code required that “across the top of each page after the first page of every initiative … petition or section thereof … there shall be printed in eighteen-point gothic type a short title….” (Id. at pp. 203-304, 34 P.2d 134.) The Supreme Court found “[i]n actual size there is a difference of but six-seventy-seconds of an inch. Only one with very poor eyesight would be unable to read a line printed in twelve-point type as readily as one printed in eighteen-point type.” (Id. at p. 204, 34 P.2d 134.) “[W]e are of the view there has been a sufficiently substantial compliance with the statute to require him to accept and file the petition.” (Ibid.; see also Othmer v. City Council of Long Beach (1929) 207 Cal. 263, 270, 277 P. 857 [finding substantial compliance where “there was nothing in the duplicate copies of the petition to mislead the electors, and there can be no doubt that each signer fully understood that he was signing a petition for the recall of the four councilmen”]; Chase v. Brooks (1986) 187 Cal.App.3d 657, 664, 232 Cal.Rptr. 65 [finding caption to be in substantial compliance with requirements].)
One reason to distinguish between information and emphasis when applying the substantial compliance doctrine is that only the latter is necessarily content neutral. Where the information is mischaracterized the electorate is misled, and the voter is unable to intelligently exercise his or her right to vote, the “sword of democracy.” (San Francisco Forty-Niners v. Nishioka, supra, 75 Cal.App.4th at p. 643, 89 Cal.Rptr.2d 388.) On the other hand, where the only defect is that the typeface is not in strict compliance with the Elections Code, the voter may still be able to intelligently exercise **363 his or her right to vote. (See California Teachers Assn. v. Collins, supra, 1 Cal.2d 202, 34 P.2d 134.) “The law is clear that election officials have a ministerial duty to reject initiative petitions which suffer from a substantial, as opposed to a technical, statutory defect which directly affects the quality of information provided to the voters.” (San Francisco Forty-Niners v. Nishioka, supra, 75 Cal.App.4th at p. 644, 89 Cal.Rptr.2d 388.)

From what I know of the distinctions between the actual text and circulated text of the initiative, it appears, especially under precedents like Mervyn‘s, that the courts would well hold the initiative should be disqualified.