This excellent source sheet produced by R. Anthony Manning, lists a number of different approaches to resolving the discrepancy:
1. Seder Olam is correct and the conventional chronology is incorrect.
Conventional chronology is incorrect due to Christian manipulation (R. Sa'adia Gaon) or Greek manipulation (R. Alexander Hool).
2. Conventional chronology is correct and Seder Olam is incorrect.
To quote directly from footnote 1 in R. Manning's source sheet:
Mitchel First’s book gives a comprehensive account of over 100 different Jewish responses on this issue! He lists a number of respected orthodox thinkers who take different positions. These include: (i) some who follow the C.C. [conventional chronology] without even mentioning S.O. [Seder Olam], such as R. Hertz in his Chumash, R. Shlomo Riskin, and R. Emmanuel Rackman; (ii) some who quote both systems, without deciding in either direction, such as R. Aryeh Kaplan and R. Ya’akov Meidan; (iii) some who consider that S.O. is not to be taken literally, such as R. Mordechai Breuer ... It is interesting to note that the Da’at Mikrah Tanach published by Mossad HaRav adopts C.C.
Mitchell First's book mentioned above is the one listed here on amazon.com.
3. Conventional chronology is correct and Seder Olam was intentionally adjusted.
Seder Olam was adjusted in order to obscure the date of the Messiah's arrival (R. Shimon Schwab), to line up the '2000 years of Torah' with the production of the Mishnah (Epstein / Dickman / Wilamowsky), to connect the Jewish year count with the 'minyan shtarot' system (R. Menachem Leibtag), or to hide the failures of the Jews to return to Zion at the start of the Second Temple period (R. Menachem Leibtag).
A full discussion of this complex historical problem is found in the article 'Missing Years' in Religion-wiki: religion.wikia.com/wiki/Missing_years. It mentions that the following sources have been taken into consideration to support the traditional dating of Seder Olam:
The internal chronology of the Hebrew Bible.
Transmitted tradition regarding the dates of annually commemorated events.
The Tannaitic chronicle Seder Olam Rabba and later chronicles such as the Seder Olam Zuta, Seder_Ha-Dorot and Toldot Am Olam.
Comments on historical events in other Jewish writings such as the Talmud and the commentaries of Rashi.
The secular Greek writings of the Jewish historian Josephus and the national traditions preserved by the Persian historian Firdausi.
The Greek, Babylonian and Persian sources cited by those supporting the secular dating, but interpreted in a manner consistent with the traditional dating.
And it concludes by saying: 'This approach to the discrepancy is the most problematic. The reinterpretation of the Greek, Babylonian and Persian sources that is required to support the traditional dating has been achieved only in parts and has not yet been achieved in its entirety.'
Jewish Encyclopedia in the article 'Seder Olam' has a brief discussion, asserting that Seder Olam's handling of the Persian period is 'contrary to historical facts':
The 420 years of the Second Temple are divided into the following periods: the domination of the Persians, 34 years; of the Greeks, 180 years; of the Maccabees, 103 years; of the Herods, 103 years. It will be seen that the allowance, contrary to historical facts, of only thirty-four years for the Persian domination is necessary if agreement with the Biblical text is to be insisted upon; for it is stated (Dan. ix. 24) that the second exile was to take place after seventy Sabbaths of years (= 490 years). If from this number the seventy years of the first Captivity be deducted, and the beginning of Alexander's domination over Palestine be placed, in accordance with Talmudical evidence, at 386 years before the destruction of the Second Temple, there remain only thirty-four for the Persian rule.
Suggested Further Reading: Seder Olam: The Rabbinic View of Biblical Chronology, Heinrich Guggenheimer, editor. (Lanham: Rowman and Littlefield, 2005).