The controversy goes back to the question of whether Manchuria is an integral and historic part of China. Right after the 1911 Revolution, the revolutionaries did not tend to think it was. Hence their willingness to contemplate 'deporting' all Manchus to Manchuria and excluding Manchuria from the new Chinese republic. After all, it was the homeland of a foreign people who had invaded and conquered China.
But the ROC government realized that letting Manchuria become an independent country would be tantamount to giving Russia or Japan a chance to make it a client state, and from there pose a threat to China. So the ROC incorporated Manchuria into its territory and encouraged more Han immigration to the region (which IIRC had already grown rapidly in the last years of the Qing when non-Manchu settlement in Manchuria was legalized). The ROC also promoted a new conception of Chinese nationhood, a Republic of Five Races (including the Manchus), so as to uphold the legitimacy of state borders that were inherited from the Qing empire.
In the early 1930s, Japan did try to justify its occupation of Manchuria by arguing that Manchuria was never part of China before the Qing, and thus rightfully belonged to the Manchu people alone. This led to the Manchukuo project. The ROC historian Fu Sinian led a team in writing "The Draft History of the Northeast" in 1932, which used many distortions of the historical record to 'prove' to the Lytton Commission that "the Northeast" (Manchuria) had been governed by Chinese dynasties since the beginning of recorded history.
The obvious flimsiness of the historical arguments used by Fu Sinian led other historians in the 1930s and 1940s to use a different approach in which the Manchus were Chinese because like the Han, Mongols, Hui, and Tibetans, they were all descended from the Yellow Emperor (Huangdi). They were thus just different branches of the same Zhonghua (Chinese) race.
The PRC has adopted a different approach to the question of who was historically Chinese: since the early 1980s, the official position has been that all ethnic groups living within the borders of the Qing empire at its height were naturally part of the Chinese nation, and therefore Chinese. The basis for this is the argument that the expansion of the Qing empire followed natural laws of history, such as the prior existence of strong economic and cultural ties between the Qing empire and those peoples whom it conquered. Therefore the Qing period marked the final complete unification of a Chinese nation that had previously never been under a single government.
The PRC argument is, of course, far too teleological and ideologically-motivated to be acceptable to historians outside China.
So the short answer to your question is: no, the Manchus have not always been considered Chinese, but since the early 20th century they have been considered Chinese because Manchuria for political reasons has to be considered Chinese.
No prizes for guessing how I voted in the poll