When Jiraiya unsealed Five Elements Seal Naruto easily walked on water. Could it be that Eight Trigrams Seal was reason why Naruto couldn't control his chakra properly?
Not exactly, Naruto's 8 Trigram seal was placed onto him by the Fourth Hokage in order to seal the Nine-Tails inside of him. The 5 pronged seal you're referring to was placed onto him by Orochimaru in Ch 49 during Squad 7's confrontation with him in the forest of death during the Chunin exam.
As we see, Orochimaru is in the midst of his mission to inflict his curse mark onto the heir of the Uchiha, Sasuke who he has chosen to be his next host. Running into the Jinchuriki of the Nine-tails was an unexpected boon and Orochimaru opportunistically applies a seal over the already existing seal to further restrict the Chakra flow. In the panels before Jiraiya undoes the seal in Ch 90 he notes obstructive nature of the double seals.
In the panel below that, Jiraiya correctly suspects Orochimaru is the one who added the 5 prong seal. Naruto has always had trouble with precise Chakra control unlike Sakura and often Sasuke but he hasn't been hard-stuck like he was while learning water-walking before.
It's not exactly that seal from the Yondaime Hokage. Naruto has always had poor chakra control because he had so much of it. Kakashi in Naruto Shippuuden said that he has 5 times more chakra than himself. Additionally, he has Kurama chakra :) The 5 Trigrams seal disturbed Naruto's chakra control even more;)