Leo Apotheker’s surprise departure from SAP less than a year after taking over the CEO top job hints that all is not well at the software vendor.

His resignation – by “mutual agreement” – came Sunday night after the company’s supervisory board decided not to renew his contract.

Apotheker’s short tenure as CEO saw him preside over a dismal financial performance in 2009 with revenue falling 8% and software licence revenue tumbling 28% after years of growth.

It also witnessed the company cave into customer demand and curb plans to hike support costs. Customer outrage meant SAP back-tracked on plans to upgrade all customers to “enterprise” support, instead giving them the choice of sticking with the cheaper basic software backup if they preferred. With upgrades, support and maintenance major cash cows for the company, this was clearly a blow to the company’s fortunes.

Further rumblings of discontent over the clarity of its long-term strategy from customers seemed to seal his fate.

The company statement emphasised that co-founder Hasso Plattner would “continue to play a strong role in advising the new leaders on technology and product development.”  Plattner’s decision to step forward into a more active role recently could be an indication that perhaps he had not always seen eye-to-eye on product direction with Apotheker.