You problem could be anything. Firstly understand that a code reader (assuming you have a fault code stored) will tell you where the fault is being reported from. It will NOT necessarily tell you what is at fault. It does not work like that.
One possibility is that the engine has sticking valves. This may be reported as P0300 - Random Misfire. This is because the ECM detects a misfire via erratic O2 sensor information, but cannot specifically pin it down. Sticking valves usually occurs shortly after a cold start, and is more likely to occur on an engine that predominantly does short runs. A scantool would be useful to test for this. Check the MAP sensor reading on live data with the engine idling. The reading should show a steady pressure of 40KPa or thereabouts. It could be a couple of KPa either way, but that doesn't really matter. What does matter is that the reading is steady. A fluctuating reading would indicate sticking valves.
On a modern car this problem is a double whammy. Not only would you have a loss of compression but the MAP sensor would not give a correct pressure reading to the ECM, which would greatly upset the fuelling.
A scantool is essential on a modern car, not only for checking fault codes, but for checking live data.
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